Neonatal Analysis

This document chronicles the analysis from the data as it is exported as median signaling and event counts from nolanlab.cytobank.org.

Cleaning the data

Load the necessary packages:

library(dplyr)
library(reshape2)
library(tidyr)
library(blackbuck)
library(FDAlibrary)
library(ggplot2)
library(samr)

Load the signaling data:

setwd("~/Documents/neonatal")
dataDirectory <- "./exported_statistics/"
raw_df <- read.csv(paste(dataDirectory, "neonatals-medians.csv", sep = ""))
figure_directory <- "./figure_graphs/"

Clean Cytobank output for our uses.

raw_df <- raw_df %>%
  tidyr::separate(col = Conditions, into = c("SampleType", "Conditions"), sep = "_") %>%
  dplyr::select(-(FCS.Filename)) %>%
  dplyr::rename(Pair = Individuals) %>%
  dplyr::mutate(Individual = as.factor(paste(Pair, SampleType, sep = "_"))) %>%
  dplyr::rename(Condition = Conditions) %>%
  dplyr::select(-contains("Singlets")) %>%
  dplyr::select(-contains("Mononuclear"))
annotation_columns = c("Individual", "Pair","SampleType", "Condition")

Now we have the following attributes as columns

• Individual = which subject
• Pair = which mother-baby pair the subject belongs to (e.g. uc01)
• SampleType = mother or baby (B or M)
• Condition = stimulation condition (Unstim, LPS, or Cocktail)

Name cleaning:

Generate fold change data (arcsinh ratio) for LPS and cocktail:

fold_df <- get_folds(raw_df, basal_name = "unstim", fold_type = "asinh", unique_IDs = "filename",
                     annotation_columns = annotation_columns)
LPS_df <- dplyr::filter(fold_df, Condition == "LPS")
Cocktail_df <- dplyr::filter(fold_df, Condition == "Cocktail")

And select and transform the unstim data:

unstim_df <- dplyr::filter(raw_df, Condition == "unstim")
unstim_df <- reshape2::melt(unstim_df)
unstim_df$value <- asinh(unstim_df$value / 5)
unstim_df <- reshape2::dcast(unstim_df, ... ~ variable)
unstim_df <- dplyr::select(unstim_df, -filename)
Unstim_df <- unstim_df

Now we have data frames corresponding to each condition (Unstim_df, LPS_df, and Cocktail_df) to work with in the analysis.

We additionally want to load and clean the abundance data and calculate percent totals.

setwd("~/Documents/neonatal/")
abundance_df <- read.csv(paste(dataDirectory, "neonatals-abundances.csv", sep = ""))
abundance_df <- abundance_df %>%
  tidyr::separate(col = Conditions, into = c("SampleType", "Conditions"), sep = "_") %>%
  dplyr::select(-(FCS.Filename)) %>%
  dplyr::rename(Pair = Individuals) %>%
  dplyr::mutate(Individual = as.factor(paste(Pair, SampleType, sep = "_"))) %>%
  dplyr::rename(Condition = Conditions)  %>%
  dplyr::filter(Condition == "unstim")

Calculate percentages:

base_counts <- abundance_df$Mononuclearcells_EventCounts
singlet_counts <- abundance_df$Singlets_EventCounts
cell_types <- abundance_df[,!(names(abundance_df) %in% c(annotation_columns, 
                                                         "Singlets_EventCounts", 
                                                         "Mononuclearcells_EventCounts", 
                                                         "Granulocytes_EventCounts", "filename"))]
grans <- abundance_df$Granulocytes_EventCounts
percents <- cbind(cell_types/base_counts, Granulocytes_EventCounts = grans/singlet_counts)
percents_df <- data.frame(filename = abundance_df$filename, abundance_df[, colnames(abundance_df) %in% annotation_columns], percents)
# write.csv(percents_df, file = "~/Documents/neonatal/neonatals_percentages.csv")

Now the data frame percents_df has the percent totals of all populations as percentage of mononuclear cells, with the exception of granulocytes which are as a percent of singlets.

Name cleaning for abundances:

Frequency differences between Mom and Baby populations using SAM paired

Generate response varaible y for Two Class Paired (Mom and Baby)

# SAMDirectory <- "~/Documents/neonatal/SAM/"
y <- dplyr::select(unstim_df, Pair, SampleType)
y <- cbind(y, resp = rep(1:10, each  = 2))
for (i in 1:nrow(y)){
  if ( y[i, "SampleType"] == "B"){
    y[i, "resp"] <- -(y[i, "resp"])
  }
}
y <- y$resp

Run SAM model

# generated percents_df (includes annotations) and percents (numeric only) 
x <- percents
runSAM <- function(){
  sink("/dev/null")
model <-  SAM(t(x), y, genenames = colnames(x), resp.type = "Two class paired", nperms = 1000, fdr.output = 0.01)
sink()
return(model)
}
model <- runSAM()
sig.up <- model$siggenes.table$genes.up[model$siggenes.table$genes.up[,"q-value(%)"] == "0", ]
# Higher in Mom
print(sig.up)

##      Gene ID                            Gene Name Score(d) Numerator(r)
## [1,] "Memory_CD4_T_cells_Percent_Total" "18"      "6.219"  "0.096"     
## [2,] "CD8_T_cells_Percent_Total"        "1"       "4.465"  "0.078"     
## [3,] "Memory_CD8_T_cells_Percent_Total" "5"       "4.007"  "0.059"     
## [4,] "Granulocytes_Percent_Total"       "19"      "3.361"  "0.135"     
## [5,] "Th1_T_cells_Percent_Total"        "11"      "2.757"  "0.019"     
## [6,] "gd_T_cells_Percent_Total"         "17"      "2.336"  "0.009"     
## [7,] "Naive_CD8_T_cells_Percent_Total"  "4"       "2.115"  "0.02"      
##      Denominator(s+s0) Fold Change q-value(%)
## [1,] "0.015"           "2.163"     "0"       
## [2,] "0.017"           "1.555"     "0"       
## [3,] "0.015"           "2.82"      "0"       
## [4,] "0.04"            "1.452"     "0"       
## [5,] "0.007"           "13.376"    "0"       
## [6,] "0.004"           "3.112"     "0"       
## [7,] "0.009"           "1.181"     "0"

sig.lo <- model$siggenes.table$genes.lo[model$siggenes.table$genes.lo[,"q-value(%)"] == "0", ]
# Higher in Baby
print(sig.lo)

##      Gene ID                           Gene Name Score(d) Numerator(r)
## [1,] "B_cells_Percent_Total"           "6"       "-6.613" "-0.104"    
## [2,] "Naive_CD4_T_cells_Percent_Total" "3"       "-2.929" "-0.094"    
## [3,] "CD56lo_NK_cells_Percent_Total"   "15"      "-1.957" "-0.007"    
## [4,] "MDSCs_Percent_Total"             "13"      "-1.858" "-0.008"    
##      Denominator(s+s0) Fold Change q-value(%)
## [1,] "0.016"           "0.457"     "0"       
## [2,] "0.032"           "0.708"     "0"       
## [3,] "0.004"           "0.669"     "0"       
## [4,] "0.004"           "0.536"     "0"

sigs <- rbind(sig.up, sig.lo)
# write.csv(sigs, file = paste(SAMDirectory,  "percent_mononuclear_fdr_0.01.csv", sep = ""))

df <- percents_df
sig_df <- data.frame(sigs)
feat_vals <- cbind(Individual = df$Individual, df[, colnames(df) %in% sig_df$Gene.ID])
# write.csv(feat_vals, file = paste(SAMDirectory, "percent_mononuclear_feature_values_fdr_0.01.csv", sep = ""))

df <- melt(df)

## Using filename, SampleType, Condition, Pair, Individual as id variables

df <- df[df[, "variable"] %in% sig_df$Gene.ID,]
ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Abundance differences (% Mononuclear cells)") + coord_flip()

# log scale
ggplot(df, aes(variable, log10(value))) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Abundance differences (% Mononuclear cells)") + coord_flip() + scale_color_brewer(palette = "Dark2") + theme_bw()

# #ggsave(filename = paste(figure_directory, "abundances_sig_plot.pdf", sep = ""), width = 10, height = 10,  useDingbats=FALSE)

# #ggsave(filename = paste(figure_directory, "abundances_sig_plot2.pdf", sep = ""), width = 30, height = 20,  useDingbats=FALSE)

# plot all
df <- percents_df
df <- reshape2::melt(df)

## Using filename, SampleType, Condition, Pair, Individual as id variables

ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Abundance differences (% Mononuclear cells)") + coord_flip()

# log scale
ggplot(df, aes(variable, log10(value))) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Abundance differences (% Mononuclear cells)") + coord_flip() + scale_color_brewer(palette = "Dark2") + theme_bw()

# #ggsave(filename = paste(SAMDirectory, "percent_mononuclear_all_plot.pdf", sep = ""), width = 30, height = 20)

Features that are not significant based on the estimated Q-val = 0:

not_sig <- percents_df[,!(colnames(percents_df) %in% sig_df$Gene.ID)]
colnames(dplyr::select(not_sig, contains("EventCounts")))

## character(0)

Might want to include Scaffold in this figure.

Confidence intervals: (1 is significant, i.e. interval does not include zero)

mom_df <- percents_df %>% dplyr::filter(SampleType == "M") %>% dplyr::select(-filename, -Pair, -SampleType, -Condition, -Individual)
baby_df <- percents_df %>% dplyr::filter(SampleType == "B") %>% dplyr::select(-filename, -Pair, -SampleType, -Condition, -Individual)
conf_int <- mapply(function(x, y) t.test(x,y, paired = TRUE)$conf.int[1:2], mom_df, baby_df)
conf_int <- t(conf_int)
colnames(conf_int) <- c("lower_bound", "upper_bound")
interval_no_zero <- sign(conf_int[, "lower_bound"]) == sign(conf_int[, "upper_bound"])
cbind(conf_int, interval_no_zero)

##                                        lower_bound   upper_bound
## CD8_T_cells_Percent_Total             0.0401081357  1.155168e-01
## CD4_T_cells_Percent_Total            -0.0807887193  8.351260e-02
## Naive_CD4_T_cells_Percent_Total      -0.1644497247 -2.308146e-02
## Naive_CD8_T_cells_Percent_Total       0.0003669442  3.870683e-02
## Memory_CD8_T_cells_Percent_Total      0.0273439822  9.032883e-02
## B_cells_Percent_Total                -0.1372103743 -6.983107e-02
## Classical_monocytes_Percent_Total    -0.0523618634  4.152444e-02
## Nonclassical_monocytes_Percent_Total -0.0016454460  4.994231e-03
## cDCs_Percent_Total                   -0.0425593280  5.395465e-02
## pDCs_Percent_Total                    0.0004260802  1.508539e-03
## Th1_T_cells_Percent_Total             0.0051520612  3.309257e-02
## Intermediate_monocytes_Percent_Total -0.0019590055  4.552569e-03
## MDSCs_Percent_Total                  -0.0154941425 -3.119472e-05
## Tregs_Percent_Total                  -0.0039976574  1.249058e-03
## CD56lo_NK_cells_Percent_Total        -0.0130613427 -6.530414e-04
## CD56hi_NK_cells_Percent_Total        -0.0004596581  3.247199e-03
## gd_T_cells_Percent_Total              0.0020075346  1.602777e-02
## Memory_CD4_T_cells_Percent_Total      0.0628400793  1.292807e-01
## Granulocytes_Percent_Total            0.0458562559  2.242088e-01
##                                      interval_no_zero
## CD8_T_cells_Percent_Total                           1
## CD4_T_cells_Percent_Total                           0
## Naive_CD4_T_cells_Percent_Total                     1
## Naive_CD8_T_cells_Percent_Total                     1
## Memory_CD8_T_cells_Percent_Total                    1
## B_cells_Percent_Total                               1
## Classical_monocytes_Percent_Total                   0
## Nonclassical_monocytes_Percent_Total                0
## cDCs_Percent_Total                                  0
## pDCs_Percent_Total                                  1
## Th1_T_cells_Percent_Total                           1
## Intermediate_monocytes_Percent_Total                0
## MDSCs_Percent_Total                                 1
## Tregs_Percent_Total                                 0
## CD56lo_NK_cells_Percent_Total                       1
## CD56hi_NK_cells_Percent_Total                       0
## gd_T_cells_Percent_Total                            1
## Memory_CD4_T_cells_Percent_Total                    1
## Granulocytes_Percent_Total                          1

Examining signaling variance with PCA

Running PCA on entire signaling dataset:

dfs <- list("LPS" = LPS_df, "Cocktail" = Cocktail_df, "Unstim" = Unstim_df)
df <- do.call(cbind, args = dfs)
df_num <- df %>% dplyr::select(-contains("Individual"), -contains("Pair"), - contains("SampleType"), -contains("Condition"))
x <- as.matrix(df_num)

pr.out <- prcomp(x, scale = FALSE)
transformed_x <- pr.out$x
PC_df <- data.frame(transformed_x, Individual = unstim_df$Individual, SampleType = unstim_df$SampleType, Pair = unstim_df$Pair)
loadings1 <- pr.out$rotation[, "PC1"]
loadings2 <- pr.out$rotation[, "PC2"]

Plotting PCA, coloring by population shows that PC1 separates the Mom and Baby populations:

# plotting
pca <- ggplot(PC_df, aes(PC1, PC2, group = Pair))
pca + geom_point(size = 2, aes(colour = SampleType)) + scale_color_brewer(palette = "Dark2") + theme_bw() + ggtitle("PCA by population")

#ggsave(paste(figure_directory, "PCA_by_population.pdf"), width = 5, height = 4,  useDingbats=FALSE)

PC2 separates by pair:

pca + geom_point(size = 2, aes(colour = Pair)) + ggtitle("PCA by mom-baby pair") + geom_line(aes(colour = Pair))

# #ggsave(paste(pairedDirectory, "PCA_by_pair.pdf"))

PC_df$Pair = factor(PC_df$Pair,levels(PC_df$Pair)[order(dplyr::filter(PC_df, SampleType == "M")$PC2)])
pca <- ggplot(PC_df, aes(Pair, PC2))
pca + geom_point(size = 2, aes(colour = Pair)) + ggtitle("PCA paired")

# #ggsave(paste(pairedDirectory, "PCA_by_pair_2.pdf"))

Variance explained by each PCA:

summary(pr.out)

## Importance of components:
##                           PC1    PC2    PC3     PC4     PC5     PC6
## Standard deviation     2.0863 1.3810 1.1638 1.02325 0.89607 0.75204
## Proportion of Variance 0.3549 0.1555 0.1104 0.08537 0.06547 0.04612
## Cumulative Proportion  0.3549 0.5104 0.6208 0.70621 0.77168 0.81780
##                            PC7     PC8     PC9    PC10    PC11    PC12
## Standard deviation     0.65190 0.53559 0.51752 0.47490 0.44968 0.40364
## Proportion of Variance 0.03465 0.02339 0.02184 0.01839 0.01649 0.01328
## Cumulative Proportion  0.85245 0.87584 0.89768 0.91607 0.93256 0.94584
##                           PC13   PC14   PC15    PC16    PC17    PC18
## Standard deviation     0.35476 0.3520 0.3341 0.29966 0.29328 0.27401
## Proportion of Variance 0.01026 0.0101 0.0091 0.00732 0.00701 0.00612
## Cumulative Proportion  0.95611 0.9662 0.9753 0.98264 0.98965 0.99577
##                           PC19      PC20
## Standard deviation     0.22775 1.546e-15
## Proportion of Variance 0.00423 0.000e+00
## Cumulative Proportion  1.00000 1.000e+00

Loadings of PC1 (highest 10):

print(sort(loadings1, decreasing = TRUE)[1:10])

##  Cocktail.Intermediate_monocytes_STAT1 
##                              0.1992966 
##     Cocktail.Classical_monocytes_STAT1 
##                              0.1976372 
##                    Cocktail.cDCs_STAT1 
##                              0.1934434 
##         Cocktail.CD56lo_NK_cells_STAT1 
##                              0.1875193 
##                   Cocktail.MDSCs_STAT1 
##                              0.1756623 
##         Cocktail.CD56hi_NK_cells_STAT1 
##                              0.1745569 
##      Unstim.Nonclassical_monocytes_ERK 
##                              0.1744094 
## Unstim.Nonclassical_monocytes_MAPKAPK2 
##                              0.1480448 
##                   Cocktail.Tregs_STAT1 
##                              0.1461109 
##    Unstim.Nonclassical_monocytes_STAT1 
##                              0.1419455

Loadings of PC2 (highest 10):

print(sort(loadings2, decreasing = TRUE)[1:10])

##     Cocktail.CD56lo_NK_cells_STAT1                       LPS.pDCs_p38 
##                         0.17059745                         0.16769165 
##               Cocktail.Tregs_STAT1     Cocktail.CD56hi_NK_cells_STAT1 
##                         0.15066615                         0.11878973 
## Cocktail.Classical_monocytes_STAT1      Unstim.Classical_monocytes_S6 
##                         0.11667543                         0.11598467 
##                Cocktail.cDCs_STAT1                     Unstim.cDCs_S6 
##                         0.11521778                         0.11119839 
##          Cocktail.gd_T_cells_STAT1         Cocktail.CD4_T_cells_STAT1 
##                         0.10436562                         0.09789317

Figure 3: Signaling Differences between Mom and Baby (SAM paired)

The basal condition reflects what is occuring at steady state (versus stimulated). We additionally have the stimulated conditions (LPS and Cocktail).

dfs <- list("LPS" = LPS_df, "Cocktail" = Cocktail_df, "Unstim" = Unstim_df)
neonatal_SAM <- function(dfs, y, resp.type, SAMDirectory){
  output <- list()
  for (i in 1:length(dfs)){
    df <- dfs[[i]]
    x <- df[,!(names(df) %in% annotation_columns)]
    sink("/dev/null")
    model <-  SAM(t(x), y, genenames = colnames(x), resp.type = resp.type, nperms = 1000, fdr.output = 0.01)
    sink()
    sig.up <- model$siggenes.table$genes.up[model$siggenes.table$genes.up[,"q-value(%)"] == "0", ]
    
    
    sig.lo <- model$siggenes.table$genes.lo[model$siggenes.table$genes.lo[,"q-value(%)"] == "0", ]

    sigs <- rbind(sig.up, sig.lo)
    # write.csv(sigs, file = paste(SAMDirectory, names(dfs)[i], "_fdr_0.01.csv", sep = ""))
    output[[names(dfs)[i]]] <- sigs
    
    sig_df <- data.frame(sigs)
    feat_vals <- cbind(Individual = df$Individual, df[, colnames(df) %in% sig_df$Gene.ID])
    # write.csv(feat_vals, file = paste(SAMDirectory, names(dfs)[i], "_feature_values_fdr_0.01.csv", sep = ""))
    
    df <- melt(df)
    df <- df[df[, "variable"] %in% sig_df$Gene.ID,]
    p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle(names(dfs)[i]) + coord_flip() + theme(axis.text = element_text(size = 5))
    print(p)
    # #ggsave(filename = paste(SAMDirectory, names(dfs)[i], "_sig_plot.pdf", sep = ""), width = 30, height = 20)
    print(names(dfs)[i])
    print("Higher in Mother")
    print(sig.up[, "Gene ID"])
    print("Higher in Baby")
    print(sig.lo[, "Gene ID"])
  }
  return(output)
}

paired_output <- neonatal_SAM(dfs, y, resp.type = "Two class paired", SAMDirectory = "./SAM/")

## Using Individual, Pair, SampleType, Condition as id variables

## [1] "LPS"
## [1] "Higher in Mother"
##  [1] "Granulocytes_MAPKAPK2"        "Intermediate_monocytes_CREB" 
##  [3] "Granulocytes_NFkB"            "cDCs_ERK"                    
##  [5] "Granulocytes_p38"             "Nonclassical_monocytes_S6"   
##  [7] "Th1_T_cells_IkB"              "Classical_monocytes_ERK"     
##  [9] "Intermediate_monocytes_S6"    "Memory_CD8_T_cells_S6"       
## [11] "Granulocytes_STAT1"           "Intermediate_monocytes_ERK"  
## [13] "Th1_T_cells_STAT1"            "Th1_T_cells_STAT5"           
## [15] "Nonclassical_monocytes_CREB"  "cDCs_MAPKAPK2"               
## [17] "Th1_T_cells_STAT3"            "Th1_T_cells_CREB"            
## [19] "Classical_monocytes_MAPKAPK2" "CD56lo_NK_cells_CREB"        
## [21] "Memory_CD8_T_cells_CREB"      "B_cells_ERK"                 
## [23] "Th1_T_cells_ERK"              "pDCs_S6"                     
## [25] "pDCs_ERK"                     "Memory_CD4_T_cells_p38"      
## [27] "Tregs_STAT1"                  "Th1_T_cells_p38"             
## [29] "CD56hi_NK_cells_CREB"         "Granulocytes_CREB"           
## [31] "Tregs_CREB"                   "Th1_T_cells_S6"              
## [33] "CD56hi_NK_cells_ERK"          "Th1_T_cells_MAPKAPK2"        
## [35] "pDCs_STAT3"                   "Tregs_ERK"                   
## [37] "Tregs_p38"                    "cDCs_p38"                    
## [39] "B_cells_STAT5"                "cDCs_CREB"                   
## [41] "Naive_CD4_T_cells_ERK"        "Intermediate_monocytes_IkB"  
## [1] "Higher in Baby"
## NULL

## Using Individual, Pair, SampleType, Condition as id variables

## [1] "Cocktail"
## [1] "Higher in Mother"
##  [1] "Classical_monocytes_STAT1"    "cDCs_STAT1"                  
##  [3] "Tregs_STAT1"                  "CD56lo_NK_cells_STAT1"       
##  [5] "Naive_CD4_T_cells_STAT1"      "CD4_T_cells_STAT1"           
##  [7] "CD56hi_NK_cells_STAT1"        "Classical_monocytes_STAT3"   
##  [9] "cDCs_STAT3"                   "Intermediate_monocytes_STAT1"
## [11] "pDCs_STAT5"                   "Memory_CD4_T_cells_STAT1"    
## [13] "gd_T_cells_STAT1"             "MDSCs_STAT3"                 
## [15] "Intermediate_monocytes_CREB"  "pDCs_STAT1"                  
## [17] "Granulocytes_STAT1"           "pDCs_STAT3"                  
## [19] "Nonclassical_monocytes_STAT1" "Nonclassical_monocytes_S6"   
## [21] "Naive_CD8_T_cells_STAT1"      "CD56lo_NK_cells_STAT3"       
## [23] "Memory_CD8_T_cells_CREB"      "Intermediate_monocytes_STAT3"
## [25] "Intermediate_monocytes_S6"    "MDSCs_STAT1"                 
## [27] "Nonclassical_monocytes_CREB"  "B_cells_STAT1"               
## [29] "CD56lo_NK_cells_S6"           "Memory_CD8_T_cells_S6"       
## [31] "Th1_T_cells_ERK"              "pDCs_ERK"                    
## [33] "CD56lo_NK_cells_CREB"         "Granulocytes_NFkB"           
## [35] "CD56lo_NK_cells_ERK"          "Granulocytes_p38"            
## [1] "Higher in Baby"
##  [1] "Naive_CD8_T_cells_STAT5"         "Naive_CD4_T_cells_STAT5"        
##  [3] "Memory_CD8_T_cells_STAT3"        "CD8_T_cells_STAT5"              
##  [5] "CD8_T_cells_STAT3"               "CD4_T_cells_STAT5"              
##  [7] "gd_T_cells_STAT5"                "Memory_CD4_T_cells_STAT5"       
##  [9] "Intermediate_monocytes_MAPKAPK2" "CD56hi_NK_cells_MAPKAPK2"       
## [11] "gd_T_cells_STAT3"

## Using SampleType, Condition, Pair, Individual as id variables

## [1] "Unstim"
## [1] "Higher in Mother"
##  [1] "Intermediate_monocytes_STAT1"    "Naive_CD4_T_cells_IkB"          
##  [3] "Intermediate_monocytes_STAT5"    "CD4_T_cells_IkB"                
##  [5] "pDCs_NFkB"                       "CD4_T_cells_STAT1"              
##  [7] "Naive_CD4_T_cells_STAT1"         "Nonclassical_monocytes_STAT5"   
##  [9] "Naive_CD8_T_cells_IkB"           "Nonclassical_monocytes_STAT1"   
## [11] "Intermediate_monocytes_p38"      "Memory_CD4_T_cells_STAT1"       
## [13] "Tregs_STAT1"                     "Intermediate_monocytes_MAPKAPK2"
## [15] "Naive_CD4_T_cells_STAT5"         "CD4_T_cells_STAT5"              
## [17] "Memory_CD4_T_cells_IkB"          "Memory_CD4_T_cells_STAT5"       
## [19] "gd_T_cells_STAT1"                "Intermediate_monocytes_ERK"     
## [21] "Naive_CD8_T_cells_STAT1"         "Nonclassical_monocytes_p38"     
## [23] "Tregs_NFkB"                      "pDCs_MAPKAPK2"                  
## [25] "Memory_CD4_T_cells_NFkB"         "Nonclassical_monocytes_IkB"     
## [27] "Nonclassical_monocytes_MAPKAPK2" "cDCs_STAT5"                     
## [29] "cDCs_STAT1"                      "CD56lo_NK_cells_STAT1"          
## [31] "CD8_T_cells_STAT1"               "Tregs_STAT5"                    
## [33] "pDCs_STAT1"                      "Classical_monocytes_STAT5"      
## [35] "Classical_monocytes_STAT1"       "Nonclassical_monocytes_ERK"     
## [37] "pDCs_p38"                        "Naive_CD8_T_cells_STAT5"        
## [1] "Higher in Baby"
##  [1] "Memory_CD8_T_cells_MAPKAPK2" "B_cells_ERK"                
##  [3] "Memory_CD4_T_cells_MAPKAPK2" "Th1_T_cells_CREB"           
##  [5] "Th1_T_cells_S6"              "Naive_CD8_T_cells_ERK"      
##  [7] "CD8_T_cells_ERK"             "Tregs_S6"                   
##  [9] "Th1_T_cells_MAPKAPK2"        "CD8_T_cells_MAPKAPK2"       
## [11] "gd_T_cells_MAPKAPK2"         "B_cells_S6"                 
## [13] "CD4_T_cells_MAPKAPK2"        "CD56lo_NK_cells_S6"         
## [15] "Th1_T_cells_ERK"             "CD56hi_NK_cells_IkB"        
## [17] "B_cells_NFkB"                "Tregs_MAPKAPK2"             
## [19] "Memory_CD8_T_cells_ERK"      "CD56lo_NK_cells_CREB"       
## [21] "B_cells_STAT5"               "Naive_CD4_T_cells_MAPKAPK2" 
## [23] "Naive_CD4_T_cells_ERK"       "Naive_CD8_T_cells_MAPKAPK2" 
## [25] "Th1_T_cells_STAT3"           "B_cells_MAPKAPK2"           
## [27] "CD56hi_NK_cells_MAPKAPK2"    "Tregs_CREB"                 
## [29] "CD4_T_cells_S6"              "CD4_T_cells_ERK"            
## [31] "B_cells_CREB"                "Naive_CD8_T_cells_CREB"     
## [33] "Naive_CD4_T_cells_CREB"      "CD56hi_NK_cells_S6"         
## [35] "Granulocytes_MAPKAPK2"       "CD56hi_NK_cells_ERK"        
## [37] "Th1_T_cells_STAT5"           "CD56hi_NK_cells_CREB"       
## [39] "Memory_CD4_T_cells_S6"       "Memory_CD4_T_cells_ERK"     
## [41] "Memory_CD8_T_cells_STAT5"    "Th1_T_cells_IkB"            
## [43] "Memory_CD4_T_cells_CREB"     "Memory_CD8_T_cells_IkB"     
## [45] "CD4_T_cells_CREB"            "Naive_CD4_T_cells_S6"       
## [47] "Granulocytes_CREB"           "CD56lo_NK_cells_IkB"        
## [49] "Th1_T_cells_STAT1"           "MDSCs_CREB"                 
## [51] "cDCs_CREB"                   "Nonclassical_monocytes_S6"

Figure 4: Filtering the Signaling Condition features by mean induction

For both stimulation conditions, there are many hits, and we may want to highlight a few based on effect size. Each stimulation has a different effect size. Here we plot all the means of the significant features in the LPS condition:

sig_LPS <- LPS_df[, colnames(LPS_df) %in% paired_output$LPS[, "Gene ID"] ]
means <- apply(sig_LPS, 2, mean)
plot(sort(means), main = "LPS significant means, sorted")

# pdf(paste(figure_directory, "LPS_sorted_abs_all.pdf", sep = ""),width = 6,height = 4, useDingbats=FALSE)
plot(sort(abs(means)), main = "LPS significant means, sorted", pch = 20)
abline(a = 0.1, b = 0, col = "red", lwd = 2)

dev.off()

## null device 
##           1

Therefore if we set a cutoff of an induction of 0.1, we filter out the near-zero conditions and return the following features:

sig_feat_thresholded <- names(means[abs(means) > 0.1])



df <- melt(LPS_df)

## Using Individual, Pair, SampleType, Condition as id variables

df <- df[df[, "variable"] %in% sig_feat_thresholded,]
ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("LPS thresholded") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()

# #ggsave(paste(figure_directory, "LPS_high_in_mom.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)
print(sig_feat_thresholded)

##  [1] "Granulocytes_CREB"            "Granulocytes_p38"            
##  [3] "Granulocytes_STAT1"           "Granulocytes_MAPKAPK2"       
##  [5] "Granulocytes_NFkB"            "Classical_monocytes_MAPKAPK2"
##  [7] "Classical_monocytes_ERK"      "Nonclassical_monocytes_CREB" 
##  [9] "Nonclassical_monocytes_S6"    "cDCs_CREB"                   
## [11] "cDCs_p38"                     "cDCs_MAPKAPK2"               
## [13] "cDCs_ERK"                     "pDCs_S6"                     
## [15] "Intermediate_monocytes_CREB"  "Intermediate_monocytes_S6"   
## [17] "Intermediate_monocytes_IkB"   "Intermediate_monocytes_ERK"

# write.csv(sig_feat_thresholded, file = "~/Documents/neonatal/for_brice/LPS_SAM_higher_in_mom.csv")

All of these tend to be myeloid cells (Granulocytes, Monocyte subsets, DC subsets) signaling in MAPAKPK2, P38, CREB, ERK, S6, STAT1, IkB/NFkB. In addition, all of these are higher in mom (meaning mom has a higher innate immune signaling capacity than baby by our measurements).

We similarly can plot the Cocktail feature means to see the magnitude of induction:

df <- Cocktail_df
sig_feats <- df[, colnames(df) %in% paired_output$Cocktail[, "Gene ID"] ]
means <- apply(sig_feats, 2, mean)
plot(sort(means), main = "Cocktail significant means, sorted")

#pdf(paste(figure_directory, "Cocktail_sorted.pdf", sep = ""),width = 6,height = 4, useDingbats=FALSE)
#plot(sort(means), main = "Cocktail significant means, sorted", pch = 20)
#abline(a = 1, b = 0, col = "red", lwd = 2)
#dev.off()

Here we see a break point at arcsinh ratio of 1.0. We can filter there and get the following:

sig_feat_thresholded <- names(means[abs(means) > 1])
df <- melt(Cocktail_df)

## Using Individual, Pair, SampleType, Condition as id variables

df <- df[df[, "variable"] %in% sig_feat_thresholded,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Cocktail") + coord_flip() + theme(axis.text = element_text(size = 5))
print(p)

print(sig_feat_thresholded)

##  [1] "Granulocytes_STAT1"           "CD8_T_cells_STAT5"           
##  [3] "CD8_T_cells_STAT3"            "CD4_T_cells_STAT5"           
##  [5] "CD4_T_cells_STAT1"            "Naive_CD4_T_cells_STAT5"     
##  [7] "Naive_CD4_T_cells_STAT1"      "Naive_CD8_T_cells_STAT5"     
##  [9] "Naive_CD8_T_cells_STAT1"      "Memory_CD8_T_cells_STAT3"    
## [11] "B_cells_STAT1"                "Classical_monocytes_STAT1"   
## [13] "Classical_monocytes_STAT3"    "Nonclassical_monocytes_STAT1"
## [15] "cDCs_STAT1"                   "cDCs_STAT3"                  
## [17] "pDCs_STAT5"                   "pDCs_STAT1"                  
## [19] "pDCs_STAT3"                   "Intermediate_monocytes_STAT1"
## [21] "Intermediate_monocytes_STAT3" "MDSCs_STAT1"                 
## [23] "MDSCs_STAT3"                  "Tregs_STAT1"                 
## [25] "CD56lo_NK_cells_STAT1"        "CD56lo_NK_cells_STAT3"       
## [27] "CD56hi_NK_cells_STAT1"        "gd_T_cells_STAT5"            
## [29] "gd_T_cells_STAT1"             "gd_T_cells_STAT3"            
## [31] "Memory_CD4_T_cells_STAT5"     "Memory_CD4_T_cells_STAT1"

This is list now contains a variety of both innate and adaptive cell types but all are pSTAT1, pSTAT3, and pSTAT5 signaling. Here’s if we look at only what’s higher in mom v. only what’s higher in baby:

m <- dplyr::filter(df, SampleType == "M")
m_by <- dplyr::group_by(m, variable)
m_mean <- summarise(m_by, mean_val = mean(value))

b <- dplyr::filter(df, SampleType == "B")
b_by <- dplyr::group_by(b, variable)
b_mean <- summarise(b_by, mean_val = mean(value))

# higher in mother
m_df <- m_mean$variable[m_mean$mean_val > b_mean$mean_val]
# write.csv(m_df, file = "~/Documents/neonatal/for_brice/Cocktail_SAM_higher_in_mom.csv")
df <- melt(Cocktail_df)

## Using Individual, Pair, SampleType, Condition as id variables

df <- df[df[, "variable"] %in% m_df,]

p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Cocktail, thresholded, higher in mother") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
print(p)

# #ggsave(paste(figure_directory, "Cocktail_high_in_mom.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)


# higher in baby
b_df <- m_mean$variable[m_mean$mean_val < b_mean$mean_val]
# write.csv(b_df, file = "~/Documents/neonatal/for_brice/Cocktail_SAM_higher_in_baby.csv")

df <- melt(Cocktail_df)

## Using Individual, Pair, SampleType, Condition as id variables

df <- df[df[, "variable"] %in% b_df,]

p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Cocktail, thresholded, higher in baby") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
print(p)

# #ggsave(paste(figure_directory, "Cocktail_high_in_baby.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)

It looks like all of the higher in baby are adaptive features, whereas most of the higher in mom and innate features.

Sorting the Unstimulated condition based on the average difference between mom and baby

In this case we do not have an induction over baseline, therefore to examine the significant features we order them by the size of the difference between mom and baby:

df <- Unstim_df
sig_feats <- df[, colnames(df) %in% paired_output$Unstim[, "Gene ID"] ]
sig_feats[["SampleType"]] <- Unstim_df$SampleType
M_feats <- sig_feats %>% dplyr::filter(SampleType == "M") %>% dplyr::select(-SampleType)
B_feats <- sig_feats %>% dplyr::filter(SampleType == "B") %>% dplyr::select(-SampleType)
M_means <- apply(M_feats, 2, mean)
B_means <- apply(B_feats, 2, mean)
Diff_means <- M_means - B_means
# plot(sort(Diff_means), main = "Mean differences in unstimulated")
plot(sort(abs(Diff_means)),  main = "Mean differences in unstimulated (absolute value)")

Here we use a cut of 0.3 in magnitude based on where the slope changes:

#pdf(paste(figure_directory, "Unstim_sorted.pdf", sep = ""),width = 6,height = 4, useDingbats=FALSE)
#plot(sort(abs(Diff_means)), main = "Mean differences in unstimulated (absolute value)", pch = 20)
#abline(a = 0.3, b = 0, col = "red", lwd = 2)
#dev.off()
sig_feat_thresholded <- names(Diff_means[abs(Diff_means) > 0.3])
df <- melt(Unstim_df)

## Using SampleType, Condition, Pair, Individual as id variables

df <- df[df[, "variable"] %in% sig_feat_thresholded,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Unstim_thresholded") + coord_flip() + theme(axis.text = element_text(size = 5))
print(p)

print(sig_feat_thresholded)

##  [1] "CD8_T_cells_MAPKAPK2"            "CD8_T_cells_ERK"                
##  [3] "Naive_CD8_T_cells_ERK"           "Memory_CD8_T_cells_MAPKAPK2"    
##  [5] "B_cells_S6"                      "B_cells_ERK"                    
##  [7] "Nonclassical_monocytes_STAT1"    "Nonclassical_monocytes_MAPKAPK2"
##  [9] "Nonclassical_monocytes_ERK"      "Th1_T_cells_CREB"               
## [11] "Th1_T_cells_S6"                  "Th1_T_cells_MAPKAPK2"           
## [13] "Th1_T_cells_ERK"                 "Intermediate_monocytes_STAT1"   
## [15] "Intermediate_monocytes_ERK"      "CD56lo_NK_cells_CREB"

Here we can also split into higher in mom v. higher in baby (Unstim):

df <- df[df[, "variable"] %in% sig_feat_thresholded,]
m <- dplyr::filter(df, SampleType == "M")
m_by <- dplyr::group_by(m, variable)
m_mean <- summarise(m_by, mean_val = mean(value))

b <- dplyr::filter(df, SampleType == "B")
b_by <- dplyr::group_by(b, variable)
b_mean <- summarise(b_by, mean_val = mean(value))

# higher in mother
m_df <- m_mean$variable[m_mean$mean_val > b_mean$mean_val]
# write.csv(m_df, file = "~/Documents/neonatal/for_brice/Unstim_SAM_higher_in_mom.csv")

df <- melt(Unstim_df)

## Using SampleType, Condition, Pair, Individual as id variables

df <- df[df[, "variable"] %in% m_df,]

p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Unstim, thresholded, higher in mother") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
print(p)

# #ggsave(paste(figure_directory, "Unstim_high_in_mother.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)



# higher in baby
b_df <- m_mean$variable[m_mean$mean_val < b_mean$mean_val]
# write.csv(b_df, file = "~/Documents/neonatal/for_brice/Unstim_SAM_higher_in_baby.csv")

df <- melt(Unstim_df)

## Using SampleType, Condition, Pair, Individual as id variables

df <- df[df[, "variable"] %in% b_df,]

p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Unstim, thresholded, higher in baby") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
print(p)

# #ggsave(paste(figure_directory, "Unstim_high_in_baby.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)

Compairson Look at SAM unpaired results:

## Using Individual, Pair, SampleType, Condition as id variables

## [1] "LPS"
## [1] "Higher in Mother"
##  [1] "cDCs_ERK"                     "Intermediate_monocytes_CREB" 
##  [3] "Classical_monocytes_ERK"      "Granulocytes_MAPKAPK2"       
##  [5] "Th1_T_cells_IkB"              "Granulocytes_NFkB"           
##  [7] "cDCs_MAPKAPK2"                "Th1_T_cells_STAT1"           
##  [9] "Th1_T_cells_STAT5"            "Classical_monocytes_MAPKAPK2"
## [11] "Nonclassical_monocytes_S6"    "Intermediate_monocytes_ERK"  
## [13] "Th1_T_cells_ERK"              "B_cells_ERK"                 
## [15] "Granulocytes_p38"             "CD56lo_NK_cells_CREB"        
## [17] "Granulocytes_STAT1"           "Intermediate_monocytes_S6"   
## [19] "Th1_T_cells_STAT3"            "Th1_T_cells_CREB"            
## [21] "Memory_CD8_T_cells_S6"        "Tregs_STAT1"                 
## [23] "pDCs_S6"                      "Th1_T_cells_p38"             
## [25] "Memory_CD4_T_cells_p38"       "Memory_CD8_T_cells_CREB"     
## [27] "Tregs_CREB"                   "Tregs_p38"                   
## [29] "pDCs_STAT3"                   "Th1_T_cells_MAPKAPK2"        
## [31] "Th1_T_cells_S6"               "B_cells_STAT5"               
## [33] "CD56hi_NK_cells_ERK"          "Tregs_ERK"                   
## [35] "Intermediate_monocytes_STAT3" "pDCs_ERK"                    
## [37] "CD56hi_NK_cells_CREB"         "Naive_CD4_T_cells_ERK"       
## [39] "Memory_CD8_T_cells_p38"       "Nonclassical_monocytes_CREB" 
## [41] "pDCs_CREB"                    "Granulocytes_CREB"           
## [43] "Naive_CD4_T_cells_IkB"        "cDCs_S6"                     
## [45] "Naive_CD8_T_cells_IkB"        "Memory_CD4_T_cells_STAT1"    
## [47] "cDCs_CREB"                    "gd_T_cells_S6"               
## [49] "CD56lo_NK_cells_STAT1"        "B_cells_S6"                  
## [1] "Higher in Baby"
## NULL

## Using Individual, Pair, SampleType, Condition as id variables

## [1] "Cocktail"
## [1] "Higher in Mother"
##  [1] "Classical_monocytes_STAT1"    "cDCs_STAT1"                  
##  [3] "CD56lo_NK_cells_STAT1"        "CD56hi_NK_cells_STAT1"       
##  [5] "Naive_CD4_T_cells_STAT1"      "Classical_monocytes_STAT3"   
##  [7] "Intermediate_monocytes_STAT1" "Tregs_STAT1"                 
##  [9] "cDCs_STAT3"                   "CD4_T_cells_STAT1"           
## [11] "Memory_CD8_T_cells_CREB"      "pDCs_STAT1"                  
## [13] "pDCs_STAT5"                   "Intermediate_monocytes_CREB" 
## [15] "Intermediate_monocytes_STAT3" "MDSCs_STAT3"                 
## [17] "Memory_CD4_T_cells_STAT1"     "gd_T_cells_STAT1"            
## [19] "pDCs_STAT3"                   "Nonclassical_monocytes_CREB" 
## [21] "MDSCs_STAT1"                  "Granulocytes_STAT1"          
## [23] "Naive_CD8_T_cells_STAT1"      "Nonclassical_monocytes_S6"   
## [25] "CD56lo_NK_cells_STAT3"        "Memory_CD8_T_cells_S6"       
## [27] "Th1_T_cells_ERK"              "Intermediate_monocytes_S6"   
## [29] "CD56lo_NK_cells_CREB"         "Granulocytes_NFkB"           
## [31] "pDCs_ERK"                     "gd_T_cells_CREB"             
## [33] "B_cells_STAT1"               
## [1] "Higher in Baby"
##  [1] "Naive_CD4_T_cells_STAT5"         "Naive_CD8_T_cells_STAT5"        
##  [3] "CD8_T_cells_STAT5"               "CD4_T_cells_STAT5"              
##  [5] "Memory_CD8_T_cells_STAT3"        "Memory_CD4_T_cells_STAT5"       
##  [7] "gd_T_cells_STAT5"                "CD56hi_NK_cells_MAPKAPK2"       
##  [9] "Intermediate_monocytes_MAPKAPK2" "CD8_T_cells_STAT3"

## Using SampleType, Condition, Pair, Individual as id variables

## [1] "Unstim"
## [1] "Higher in Mother"
##  [1] "Intermediate_monocytes_STAT1"    "Intermediate_monocytes_STAT5"   
##  [3] "Naive_CD4_T_cells_STAT5"         "CD4_T_cells_STAT5"              
##  [5] "pDCs_NFkB"                       "Memory_CD4_T_cells_STAT5"       
##  [7] "Naive_CD4_T_cells_IkB"           "Intermediate_monocytes_ERK"     
##  [9] "pDCs_STAT1"                      "Nonclassical_monocytes_STAT1"   
## [11] "Intermediate_monocytes_p38"      "Tregs_STAT1"                    
## [13] "cDCs_STAT5"                      "CD4_T_cells_STAT1"              
## [15] "Naive_CD4_T_cells_STAT1"         "Classical_monocytes_STAT5"      
## [17] "gd_T_cells_STAT1"                "Nonclassical_monocytes_STAT5"   
## [19] "Memory_CD4_T_cells_STAT1"        "Intermediate_monocytes_MAPKAPK2"
## [21] "Naive_CD8_T_cells_IkB"           "cDCs_STAT1"                     
## [23] "CD4_T_cells_IkB"                 "Nonclassical_monocytes_p38"     
## [25] "Classical_monocytes_STAT1"       "Naive_CD8_T_cells_STAT1"        
## [27] "Tregs_STAT5"                     "pDCs_p38"                       
## [29] "Naive_CD8_T_cells_STAT5"         "CD56lo_NK_cells_STAT1"          
## [31] "Tregs_NFkB"                     
## [1] "Higher in Baby"
##  [1] "B_cells_ERK"                 "Th1_T_cells_CREB"           
##  [3] "Memory_CD8_T_cells_MAPKAPK2" "CD56lo_NK_cells_CREB"       
##  [5] "CD8_T_cells_ERK"             "Naive_CD8_T_cells_ERK"      
##  [7] "Th1_T_cells_S6"              "Th1_T_cells_MAPKAPK2"       
##  [9] "Th1_T_cells_ERK"             "B_cells_S6"                 
## [11] "Memory_CD8_T_cells_ERK"      "gd_T_cells_MAPKAPK2"        
## [13] "CD8_T_cells_MAPKAPK2"        "Naive_CD4_T_cells_ERK"      
## [15] "CD56hi_NK_cells_CREB"        "B_cells_CREB"               
## [17] "Th1_T_cells_STAT3"           "Memory_CD4_T_cells_MAPKAPK2"
## [19] "CD56lo_NK_cells_S6"          "Tregs_S6"                   
## [21] "Tregs_CREB"                  "Naive_CD8_T_cells_CREB"     
## [23] "CD4_T_cells_ERK"             "Granulocytes_MAPKAPK2"      
## [25] "CD56hi_NK_cells_IkB"         "B_cells_NFkB"               
## [27] "B_cells_STAT5"               "Naive_CD4_T_cells_CREB"     
## [29] "Th1_T_cells_STAT5"           "CD56hi_NK_cells_ERK"        
## [31] "MDSCs_CREB"                  "B_cells_MAPKAPK2"           
## [33] "Granulocytes_CREB"           "CD4_T_cells_MAPKAPK2"       
## [35] "Memory_CD4_T_cells_ERK"      "Tregs_MAPKAPK2"             
## [37] "CD56hi_NK_cells_MAPKAPK2"    "Naive_CD8_T_cells_MAPKAPK2" 
## [39] "cDCs_CREB"                   "Th1_T_cells_IkB"            
## [41] "CD56hi_NK_cells_S6"          "Memory_CD4_T_cells_CREB"    
## [43] "Memory_CD8_T_cells_STAT5"

Figure 5 Paired analysis: the value added by having pair-specific information

Here we examine the added value of having paired samples (samples from a mother-baby pair as opposed to a random sample) by comparing the p-values from unpaired v. paired t-tests.
New Here we also compare to doing the significance cutoff as whether SAM paired v. unpaired found it as significant. We should use SAM throughout Here’s when we do it with all the signaling data combined (original analysis: Unstim, Cocktail, LPS)

# a function to calculate significance from SAM output
SAM_significance <- function(paired_output, unpaired_output, unpaired_pvals){
  
  get_genes <- function(output){
    all_genes <- c()
    for (i in 1:length(output)){
      genes <- output[[i]][, "Gene ID"]
      gene_names <- paste(names(output)[i], genes, sep = ".")
      all_genes <- c(all_genes, gene_names)
    }
    return(all_genes)
  }
  sig_paired <- get_genes(paired_output)
  print(sig_paired)
  sig_unpaired <- get_genes(unpaired_output)
  print(sig_unpaired)

  yes_p <- names(unpaired_pvals) %in% sig_paired
  print(yes_p)
  yes_up <- names(unpaired_pvals) %in% sig_unpaired
  print(yes_up)
  
  significance <- vector(mode = "character", length = length(unpaired_pvals))
  significance[yes_p & yes_up] <- "Both"
  significance[!(yes_p) & yes_up] <- "Unpaired only"
  significance[yes_p & !(yes_up)] <- "Paired only"
  significance[!(yes_p) & !(yes_up)] <- "Not significant"
  
  return(significance)
}

# pairedDirectory <- "~/Documents/neonatal/paired/"
sampleType <- Unstim_df$SampleType

plot_p_v_up <- function(dfs, sampleType, paired_output, unpaired_output){
df <- do.call(cbind, args = dfs)
df[["SampleType"]] <- sampleType
mom_df <- df %>% dplyr::filter(SampleType == "M") %>% dplyr::select(-contains("Individual"), -contains("Pair"), - contains("SampleType"), -contains("Condition"))
baby_df <- df %>% dplyr::filter(SampleType == "B") %>%  dplyr::select(-contains("Individual"), -contains("Pair"), - contains("SampleType"), -contains("Condition"))

paired_pvals <- mapply(function(x, y) t.test(x,y, paired = TRUE)$p.value, mom_df, baby_df)
unpaired_pvals <- mapply(function(x, y) t.test(x,y, paired = FALSE)$p.value, mom_df, baby_df)

# plot(-log(unpaired_pvals), -log(paired_pvals))

# Number of comparisons: 20 cell types x 10 phosphos x 3 conditions
bonf <- .05/(ncol(mom_df))

significance <- vector(mode = "character", length = length(unpaired_pvals))
significance[(unpaired_pvals < bonf) & (paired_pvals < bonf)] <- "Both"
significance[(unpaired_pvals < bonf) & (paired_pvals > bonf)] <- "Unpaired only"
significance[(unpaired_pvals > bonf) & (paired_pvals < bonf)] <- "Paired only"
significance[(unpaired_pvals > bonf) & (paired_pvals > bonf)] <- "Not significant"

Significance_SAM <- SAM_significance(paired_output, unpaired_output, unpaired_pvals)

plot_df <- data.frame(unpaired_pvals, paired_pvals, Significance_Bonferroni = significance, Significance_SAM = Significance_SAM, Features = names(paired_pvals))

p <- ggplot(plot_df, aes(-log(unpaired_pvals), -log(paired_pvals))) + 
  geom_point(size = 1, aes(colour = Significance_Bonferroni))  + 
  scale_color_manual(values=c("blue", " dark gray", "red", "orange"))
print(p)

p <- ggplot(plot_df, aes(-log(unpaired_pvals), -log(paired_pvals))) + 
  geom_point(size = 1, aes(colour = Significance_SAM))  + 
  scale_color_manual(values=c("#1b9e77", " dark gray", "#7570b3", "#d95f02")) + ggtitle("Using SAM Significance") + theme_bw()
print(p)
# (paste(figure_directory, "scatter_paired_v_unpaired.pdf", sep = ""), width = 8, height = 7,useDingbats=FALSE)
# #ggsave(paste(pairedDirectory, "scatter_paired_unpaired.pdf", sep = ""))
# plot_df %>% dplyr::filter(Significance_SAM != "Not significant") %>% 
  # dplyr::select(-unpaired_pvals) %>%
  # dplyr::select(-paired_pvals)
return(plot_df)
}

plot_df <- plot_p_v_up(dfs = list("LPS" = LPS_df, "Cocktail" = Cocktail_df, "Unstim" = Unstim_df), sampleType = sampleType, paired_output, unpaired_output)

##   [1] "LPS.Granulocytes_MAPKAPK2"               
##   [2] "LPS.Intermediate_monocytes_CREB"         
##   [3] "LPS.Granulocytes_NFkB"                   
##   [4] "LPS.cDCs_ERK"                            
##   [5] "LPS.Granulocytes_p38"                    
##   [6] "LPS.Nonclassical_monocytes_S6"           
##   [7] "LPS.Th1_T_cells_IkB"                     
##   [8] "LPS.Classical_monocytes_ERK"             
##   [9] "LPS.Intermediate_monocytes_S6"           
##  [10] "LPS.Memory_CD8_T_cells_S6"               
##  [11] "LPS.Granulocytes_STAT1"                  
##  [12] "LPS.Intermediate_monocytes_ERK"          
##  [13] "LPS.Th1_T_cells_STAT1"                   
##  [14] "LPS.Th1_T_cells_STAT5"                   
##  [15] "LPS.Nonclassical_monocytes_CREB"         
##  [16] "LPS.cDCs_MAPKAPK2"                       
##  [17] "LPS.Th1_T_cells_STAT3"                   
##  [18] "LPS.Th1_T_cells_CREB"                    
##  [19] "LPS.Classical_monocytes_MAPKAPK2"        
##  [20] "LPS.CD56lo_NK_cells_CREB"                
##  [21] "LPS.Memory_CD8_T_cells_CREB"             
##  [22] "LPS.B_cells_ERK"                         
##  [23] "LPS.Th1_T_cells_ERK"                     
##  [24] "LPS.pDCs_S6"                             
##  [25] "LPS.pDCs_ERK"                            
##  [26] "LPS.Memory_CD4_T_cells_p38"              
##  [27] "LPS.Tregs_STAT1"                         
##  [28] "LPS.Th1_T_cells_p38"                     
##  [29] "LPS.CD56hi_NK_cells_CREB"                
##  [30] "LPS.Granulocytes_CREB"                   
##  [31] "LPS.Tregs_CREB"                          
##  [32] "LPS.Th1_T_cells_S6"                      
##  [33] "LPS.CD56hi_NK_cells_ERK"                 
##  [34] "LPS.Th1_T_cells_MAPKAPK2"                
##  [35] "LPS.pDCs_STAT3"                          
##  [36] "LPS.Tregs_ERK"                           
##  [37] "LPS.Tregs_p38"                           
##  [38] "LPS.cDCs_p38"                            
##  [39] "LPS.B_cells_STAT5"                       
##  [40] "LPS.cDCs_CREB"                           
##  [41] "LPS.Naive_CD4_T_cells_ERK"               
##  [42] "LPS.Intermediate_monocytes_IkB"          
##  [43] "Cocktail.Classical_monocytes_STAT1"      
##  [44] "Cocktail.cDCs_STAT1"                     
##  [45] "Cocktail.Tregs_STAT1"                    
##  [46] "Cocktail.CD56lo_NK_cells_STAT1"          
##  [47] "Cocktail.Naive_CD4_T_cells_STAT1"        
##  [48] "Cocktail.CD4_T_cells_STAT1"              
##  [49] "Cocktail.CD56hi_NK_cells_STAT1"          
##  [50] "Cocktail.Classical_monocytes_STAT3"      
##  [51] "Cocktail.cDCs_STAT3"                     
##  [52] "Cocktail.Intermediate_monocytes_STAT1"   
##  [53] "Cocktail.pDCs_STAT5"                     
##  [54] "Cocktail.Memory_CD4_T_cells_STAT1"       
##  [55] "Cocktail.gd_T_cells_STAT1"               
##  [56] "Cocktail.MDSCs_STAT3"                    
##  [57] "Cocktail.Intermediate_monocytes_CREB"    
##  [58] "Cocktail.pDCs_STAT1"                     
##  [59] "Cocktail.Granulocytes_STAT1"             
##  [60] "Cocktail.pDCs_STAT3"                     
##  [61] "Cocktail.Nonclassical_monocytes_STAT1"   
##  [62] "Cocktail.Nonclassical_monocytes_S6"      
##  [63] "Cocktail.Naive_CD8_T_cells_STAT1"        
##  [64] "Cocktail.CD56lo_NK_cells_STAT3"          
##  [65] "Cocktail.Memory_CD8_T_cells_CREB"        
##  [66] "Cocktail.Intermediate_monocytes_STAT3"   
##  [67] "Cocktail.Intermediate_monocytes_S6"      
##  [68] "Cocktail.MDSCs_STAT1"                    
##  [69] "Cocktail.Nonclassical_monocytes_CREB"    
##  [70] "Cocktail.B_cells_STAT1"                  
##  [71] "Cocktail.CD56lo_NK_cells_S6"             
##  [72] "Cocktail.Memory_CD8_T_cells_S6"          
##  [73] "Cocktail.Th1_T_cells_ERK"                
##  [74] "Cocktail.pDCs_ERK"                       
##  [75] "Cocktail.CD56lo_NK_cells_CREB"           
##  [76] "Cocktail.Granulocytes_NFkB"              
##  [77] "Cocktail.CD56lo_NK_cells_ERK"            
##  [78] "Cocktail.Granulocytes_p38"               
##  [79] "Cocktail.Naive_CD8_T_cells_STAT5"        
##  [80] "Cocktail.Naive_CD4_T_cells_STAT5"        
##  [81] "Cocktail.Memory_CD8_T_cells_STAT3"       
##  [82] "Cocktail.CD8_T_cells_STAT5"              
##  [83] "Cocktail.CD8_T_cells_STAT3"              
##  [84] "Cocktail.CD4_T_cells_STAT5"              
##  [85] "Cocktail.gd_T_cells_STAT5"               
##  [86] "Cocktail.Memory_CD4_T_cells_STAT5"       
##  [87] "Cocktail.Intermediate_monocytes_MAPKAPK2"
##  [88] "Cocktail.CD56hi_NK_cells_MAPKAPK2"       
##  [89] "Cocktail.gd_T_cells_STAT3"               
##  [90] "Unstim.Intermediate_monocytes_STAT1"     
##  [91] "Unstim.Naive_CD4_T_cells_IkB"            
##  [92] "Unstim.Intermediate_monocytes_STAT5"     
##  [93] "Unstim.CD4_T_cells_IkB"                  
##  [94] "Unstim.pDCs_NFkB"                        
##  [95] "Unstim.CD4_T_cells_STAT1"                
##  [96] "Unstim.Naive_CD4_T_cells_STAT1"          
##  [97] "Unstim.Nonclassical_monocytes_STAT5"     
##  [98] "Unstim.Naive_CD8_T_cells_IkB"            
##  [99] "Unstim.Nonclassical_monocytes_STAT1"     
## [100] "Unstim.Intermediate_monocytes_p38"       
## [101] "Unstim.Memory_CD4_T_cells_STAT1"         
## [102] "Unstim.Tregs_STAT1"                      
## [103] "Unstim.Intermediate_monocytes_MAPKAPK2"  
## [104] "Unstim.Naive_CD4_T_cells_STAT5"          
## [105] "Unstim.CD4_T_cells_STAT5"                
## [106] "Unstim.Memory_CD4_T_cells_IkB"           
## [107] "Unstim.Memory_CD4_T_cells_STAT5"         
## [108] "Unstim.gd_T_cells_STAT1"                 
## [109] "Unstim.Intermediate_monocytes_ERK"       
## [110] "Unstim.Naive_CD8_T_cells_STAT1"          
## [111] "Unstim.Nonclassical_monocytes_p38"       
## [112] "Unstim.Tregs_NFkB"                       
## [113] "Unstim.pDCs_MAPKAPK2"                    
## [114] "Unstim.Memory_CD4_T_cells_NFkB"          
## [115] "Unstim.Nonclassical_monocytes_IkB"       
## [116] "Unstim.Nonclassical_monocytes_MAPKAPK2"  
## [117] "Unstim.cDCs_STAT5"                       
## [118] "Unstim.cDCs_STAT1"                       
## [119] "Unstim.CD56lo_NK_cells_STAT1"            
## [120] "Unstim.CD8_T_cells_STAT1"                
## [121] "Unstim.Tregs_STAT5"                      
## [122] "Unstim.pDCs_STAT1"                       
## [123] "Unstim.Classical_monocytes_STAT5"        
## [124] "Unstim.Classical_monocytes_STAT1"        
## [125] "Unstim.Nonclassical_monocytes_ERK"       
## [126] "Unstim.pDCs_p38"                         
## [127] "Unstim.Naive_CD8_T_cells_STAT5"          
## [128] "Unstim.Memory_CD8_T_cells_MAPKAPK2"      
## [129] "Unstim.B_cells_ERK"                      
## [130] "Unstim.Memory_CD4_T_cells_MAPKAPK2"      
## [131] "Unstim.Th1_T_cells_CREB"                 
## [132] "Unstim.Th1_T_cells_S6"                   
## [133] "Unstim.Naive_CD8_T_cells_ERK"            
## [134] "Unstim.CD8_T_cells_ERK"                  
## [135] "Unstim.Tregs_S6"                         
## [136] "Unstim.Th1_T_cells_MAPKAPK2"             
## [137] "Unstim.CD8_T_cells_MAPKAPK2"             
## [138] "Unstim.gd_T_cells_MAPKAPK2"              
## [139] "Unstim.B_cells_S6"                       
## [140] "Unstim.CD4_T_cells_MAPKAPK2"             
## [141] "Unstim.CD56lo_NK_cells_S6"               
## [142] "Unstim.Th1_T_cells_ERK"                  
## [143] "Unstim.CD56hi_NK_cells_IkB"              
## [144] "Unstim.B_cells_NFkB"                     
## [145] "Unstim.Tregs_MAPKAPK2"                   
## [146] "Unstim.Memory_CD8_T_cells_ERK"           
## [147] "Unstim.CD56lo_NK_cells_CREB"             
## [148] "Unstim.B_cells_STAT5"                    
## [149] "Unstim.Naive_CD4_T_cells_MAPKAPK2"       
## [150] "Unstim.Naive_CD4_T_cells_ERK"            
## [151] "Unstim.Naive_CD8_T_cells_MAPKAPK2"       
## [152] "Unstim.Th1_T_cells_STAT3"                
## [153] "Unstim.B_cells_MAPKAPK2"                 
## [154] "Unstim.CD56hi_NK_cells_MAPKAPK2"         
## [155] "Unstim.Tregs_CREB"                       
## [156] "Unstim.CD4_T_cells_S6"                   
## [157] "Unstim.CD4_T_cells_ERK"                  
## [158] "Unstim.B_cells_CREB"                     
## [159] "Unstim.Naive_CD8_T_cells_CREB"           
## [160] "Unstim.Naive_CD4_T_cells_CREB"           
## [161] "Unstim.CD56hi_NK_cells_S6"               
## [162] "Unstim.Granulocytes_MAPKAPK2"            
## [163] "Unstim.CD56hi_NK_cells_ERK"              
## [164] "Unstim.Th1_T_cells_STAT5"                
## [165] "Unstim.CD56hi_NK_cells_CREB"             
## [166] "Unstim.Memory_CD4_T_cells_S6"            
## [167] "Unstim.Memory_CD4_T_cells_ERK"           
## [168] "Unstim.Memory_CD8_T_cells_STAT5"         
## [169] "Unstim.Th1_T_cells_IkB"                  
## [170] "Unstim.Memory_CD4_T_cells_CREB"          
## [171] "Unstim.Memory_CD8_T_cells_IkB"           
## [172] "Unstim.CD4_T_cells_CREB"                 
## [173] "Unstim.Naive_CD4_T_cells_S6"             
## [174] "Unstim.Granulocytes_CREB"                
## [175] "Unstim.CD56lo_NK_cells_IkB"              
## [176] "Unstim.Th1_T_cells_STAT1"                
## [177] "Unstim.MDSCs_CREB"                       
## [178] "Unstim.cDCs_CREB"                        
## [179] "Unstim.Nonclassical_monocytes_S6"        
##   [1] "LPS.cDCs_ERK"                            
##   [2] "LPS.Intermediate_monocytes_CREB"         
##   [3] "LPS.Classical_monocytes_ERK"             
##   [4] "LPS.Granulocytes_MAPKAPK2"               
##   [5] "LPS.Th1_T_cells_IkB"                     
##   [6] "LPS.Granulocytes_NFkB"                   
##   [7] "LPS.cDCs_MAPKAPK2"                       
##   [8] "LPS.Th1_T_cells_STAT1"                   
##   [9] "LPS.Th1_T_cells_STAT5"                   
##  [10] "LPS.Classical_monocytes_MAPKAPK2"        
##  [11] "LPS.Nonclassical_monocytes_S6"           
##  [12] "LPS.Intermediate_monocytes_ERK"          
##  [13] "LPS.Th1_T_cells_ERK"                     
##  [14] "LPS.B_cells_ERK"                         
##  [15] "LPS.Granulocytes_p38"                    
##  [16] "LPS.CD56lo_NK_cells_CREB"                
##  [17] "LPS.Granulocytes_STAT1"                  
##  [18] "LPS.Intermediate_monocytes_S6"           
##  [19] "LPS.Th1_T_cells_STAT3"                   
##  [20] "LPS.Th1_T_cells_CREB"                    
##  [21] "LPS.Memory_CD8_T_cells_S6"               
##  [22] "LPS.Tregs_STAT1"                         
##  [23] "LPS.pDCs_S6"                             
##  [24] "LPS.Th1_T_cells_p38"                     
##  [25] "LPS.Memory_CD4_T_cells_p38"              
##  [26] "LPS.Memory_CD8_T_cells_CREB"             
##  [27] "LPS.Tregs_CREB"                          
##  [28] "LPS.Tregs_p38"                           
##  [29] "LPS.pDCs_STAT3"                          
##  [30] "LPS.Th1_T_cells_MAPKAPK2"                
##  [31] "LPS.Th1_T_cells_S6"                      
##  [32] "LPS.B_cells_STAT5"                       
##  [33] "LPS.CD56hi_NK_cells_ERK"                 
##  [34] "LPS.Tregs_ERK"                           
##  [35] "LPS.Intermediate_monocytes_STAT3"        
##  [36] "LPS.pDCs_ERK"                            
##  [37] "LPS.CD56hi_NK_cells_CREB"                
##  [38] "LPS.Naive_CD4_T_cells_ERK"               
##  [39] "LPS.Memory_CD8_T_cells_p38"              
##  [40] "LPS.Nonclassical_monocytes_CREB"         
##  [41] "LPS.pDCs_CREB"                           
##  [42] "LPS.Granulocytes_CREB"                   
##  [43] "LPS.Naive_CD4_T_cells_IkB"               
##  [44] "LPS.cDCs_S6"                             
##  [45] "LPS.Naive_CD8_T_cells_IkB"               
##  [46] "LPS.Memory_CD4_T_cells_STAT1"            
##  [47] "LPS.cDCs_CREB"                           
##  [48] "LPS.gd_T_cells_S6"                       
##  [49] "LPS.CD56lo_NK_cells_STAT1"               
##  [50] "LPS.B_cells_S6"                          
##  [51] "Cocktail.Classical_monocytes_STAT1"      
##  [52] "Cocktail.cDCs_STAT1"                     
##  [53] "Cocktail.CD56lo_NK_cells_STAT1"          
##  [54] "Cocktail.CD56hi_NK_cells_STAT1"          
##  [55] "Cocktail.Naive_CD4_T_cells_STAT1"        
##  [56] "Cocktail.Classical_monocytes_STAT3"      
##  [57] "Cocktail.Intermediate_monocytes_STAT1"   
##  [58] "Cocktail.Tregs_STAT1"                    
##  [59] "Cocktail.cDCs_STAT3"                     
##  [60] "Cocktail.CD4_T_cells_STAT1"              
##  [61] "Cocktail.Memory_CD8_T_cells_CREB"        
##  [62] "Cocktail.pDCs_STAT1"                     
##  [63] "Cocktail.pDCs_STAT5"                     
##  [64] "Cocktail.Intermediate_monocytes_CREB"    
##  [65] "Cocktail.Intermediate_monocytes_STAT3"   
##  [66] "Cocktail.MDSCs_STAT3"                    
##  [67] "Cocktail.Memory_CD4_T_cells_STAT1"       
##  [68] "Cocktail.gd_T_cells_STAT1"               
##  [69] "Cocktail.pDCs_STAT3"                     
##  [70] "Cocktail.Nonclassical_monocytes_CREB"    
##  [71] "Cocktail.MDSCs_STAT1"                    
##  [72] "Cocktail.Granulocytes_STAT1"             
##  [73] "Cocktail.Naive_CD8_T_cells_STAT1"        
##  [74] "Cocktail.Nonclassical_monocytes_S6"      
##  [75] "Cocktail.CD56lo_NK_cells_STAT3"          
##  [76] "Cocktail.Memory_CD8_T_cells_S6"          
##  [77] "Cocktail.Th1_T_cells_ERK"                
##  [78] "Cocktail.Intermediate_monocytes_S6"      
##  [79] "Cocktail.CD56lo_NK_cells_CREB"           
##  [80] "Cocktail.Granulocytes_NFkB"              
##  [81] "Cocktail.pDCs_ERK"                       
##  [82] "Cocktail.gd_T_cells_CREB"                
##  [83] "Cocktail.B_cells_STAT1"                  
##  [84] "Cocktail.Naive_CD4_T_cells_STAT5"        
##  [85] "Cocktail.Naive_CD8_T_cells_STAT5"        
##  [86] "Cocktail.CD8_T_cells_STAT5"              
##  [87] "Cocktail.CD4_T_cells_STAT5"              
##  [88] "Cocktail.Memory_CD8_T_cells_STAT3"       
##  [89] "Cocktail.Memory_CD4_T_cells_STAT5"       
##  [90] "Cocktail.gd_T_cells_STAT5"               
##  [91] "Cocktail.CD56hi_NK_cells_MAPKAPK2"       
##  [92] "Cocktail.Intermediate_monocytes_MAPKAPK2"
##  [93] "Cocktail.CD8_T_cells_STAT3"              
##  [94] "Unstim.Intermediate_monocytes_STAT1"     
##  [95] "Unstim.Intermediate_monocytes_STAT5"     
##  [96] "Unstim.Naive_CD4_T_cells_STAT5"          
##  [97] "Unstim.CD4_T_cells_STAT5"                
##  [98] "Unstim.pDCs_NFkB"                        
##  [99] "Unstim.Memory_CD4_T_cells_STAT5"         
## [100] "Unstim.Naive_CD4_T_cells_IkB"            
## [101] "Unstim.Intermediate_monocytes_ERK"       
## [102] "Unstim.pDCs_STAT1"                       
## [103] "Unstim.Nonclassical_monocytes_STAT1"     
## [104] "Unstim.Intermediate_monocytes_p38"       
## [105] "Unstim.Tregs_STAT1"                      
## [106] "Unstim.cDCs_STAT5"                       
## [107] "Unstim.CD4_T_cells_STAT1"                
## [108] "Unstim.Naive_CD4_T_cells_STAT1"          
## [109] "Unstim.Classical_monocytes_STAT5"        
## [110] "Unstim.gd_T_cells_STAT1"                 
## [111] "Unstim.Nonclassical_monocytes_STAT5"     
## [112] "Unstim.Memory_CD4_T_cells_STAT1"         
## [113] "Unstim.Intermediate_monocytes_MAPKAPK2"  
## [114] "Unstim.Naive_CD8_T_cells_IkB"            
## [115] "Unstim.cDCs_STAT1"                       
## [116] "Unstim.CD4_T_cells_IkB"                  
## [117] "Unstim.Nonclassical_monocytes_p38"       
## [118] "Unstim.Classical_monocytes_STAT1"        
## [119] "Unstim.Naive_CD8_T_cells_STAT1"          
## [120] "Unstim.Tregs_STAT5"                      
## [121] "Unstim.pDCs_p38"                         
## [122] "Unstim.Naive_CD8_T_cells_STAT5"          
## [123] "Unstim.CD56lo_NK_cells_STAT1"            
## [124] "Unstim.Tregs_NFkB"                       
## [125] "Unstim.B_cells_ERK"                      
## [126] "Unstim.Th1_T_cells_CREB"                 
## [127] "Unstim.Memory_CD8_T_cells_MAPKAPK2"      
## [128] "Unstim.CD56lo_NK_cells_CREB"             
## [129] "Unstim.CD8_T_cells_ERK"                  
## [130] "Unstim.Naive_CD8_T_cells_ERK"            
## [131] "Unstim.Th1_T_cells_S6"                   
## [132] "Unstim.Th1_T_cells_MAPKAPK2"             
## [133] "Unstim.Th1_T_cells_ERK"                  
## [134] "Unstim.B_cells_S6"                       
## [135] "Unstim.Memory_CD8_T_cells_ERK"           
## [136] "Unstim.gd_T_cells_MAPKAPK2"              
## [137] "Unstim.CD8_T_cells_MAPKAPK2"             
## [138] "Unstim.Naive_CD4_T_cells_ERK"            
## [139] "Unstim.CD56hi_NK_cells_CREB"             
## [140] "Unstim.B_cells_CREB"                     
## [141] "Unstim.Th1_T_cells_STAT3"                
## [142] "Unstim.Memory_CD4_T_cells_MAPKAPK2"      
## [143] "Unstim.CD56lo_NK_cells_S6"               
## [144] "Unstim.Tregs_S6"                         
## [145] "Unstim.Tregs_CREB"                       
## [146] "Unstim.Naive_CD8_T_cells_CREB"           
## [147] "Unstim.CD4_T_cells_ERK"                  
## [148] "Unstim.Granulocytes_MAPKAPK2"            
## [149] "Unstim.CD56hi_NK_cells_IkB"              
## [150] "Unstim.B_cells_NFkB"                     
## [151] "Unstim.B_cells_STAT5"                    
## [152] "Unstim.Naive_CD4_T_cells_CREB"           
## [153] "Unstim.Th1_T_cells_STAT5"                
## [154] "Unstim.CD56hi_NK_cells_ERK"              
## [155] "Unstim.MDSCs_CREB"                       
## [156] "Unstim.B_cells_MAPKAPK2"                 
## [157] "Unstim.Granulocytes_CREB"                
## [158] "Unstim.CD4_T_cells_MAPKAPK2"             
## [159] "Unstim.Memory_CD4_T_cells_ERK"           
## [160] "Unstim.Tregs_MAPKAPK2"                   
## [161] "Unstim.CD56hi_NK_cells_MAPKAPK2"         
## [162] "Unstim.Naive_CD8_T_cells_MAPKAPK2"       
## [163] "Unstim.cDCs_CREB"                        
## [164] "Unstim.Th1_T_cells_IkB"                  
## [165] "Unstim.CD56hi_NK_cells_S6"               
## [166] "Unstim.Memory_CD4_T_cells_CREB"          
## [167] "Unstim.Memory_CD8_T_cells_STAT5"         
##   [1]  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
##  [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [34] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [45] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [56]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [67] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
##  [78] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE
##  [89] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE
## [100]  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE
## [111]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE
## [122] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
## [144]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE
## [155] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [166] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [177] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [188] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE
## [199]  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [210] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [221] FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [232]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE
## [243] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [254]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [265]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE
## [276]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [287] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE
## [298] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [309] FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE
## [320] FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE
## [331] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [342] FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE
## [353] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE
## [364]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
## [375] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [386] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE
## [397]  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE
## [408]  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE
## [419] FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE
## [430]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE
## [441]  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE
## [452]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [463]  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE
## [474]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE
## [485] FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE
## [496]  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE
## [507]  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [518] FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE
## [529]  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE
## [540] FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE
## [551] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE
## [562]  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE
##   [1]  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
##  [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [34] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [45] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
##  [56]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE
##  [67] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
##  [78] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE
##  [89] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE
## [100]  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE
## [111]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE
## [122] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
## [144]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE
## [155] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [166] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE
## [177] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE
## [188] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [199]  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [210] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [221] FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [232]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE
## [243] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [254]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [265]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [276]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [287] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE
## [298] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [309] FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE
## [320] FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE
## [331] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [342] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [353] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [364]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
## [375] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [386] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [397]  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE
## [408]  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE
## [419] FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE
## [430]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE
## [441]  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE
## [452]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [463]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [474]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE
## [485] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE
## [496]  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE
## [507]  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [518] FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE
## [529]  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE
## [540] FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE
## [551] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE
## [562]  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE

test <- strsplit(as.character(plot_df$Features), "[.]")
plot_df_new <- data.frame(plot_df, Condition = sapply(test, function(x) x[[1]]))
levels(plot_df_new$Condition) <- c(levels(plot_df_new$Condition), "Not Significant")
plot_df_new[plot_df_new$Significance_SAM == "Not significant", "Condition"] <- "Not Significant"
ggplot(plot_df_new, aes(-log(unpaired_pvals), -log(paired_pvals))) + 
  geom_point(size = 1, aes(colour = Condition))  + 
  scale_color_manual(values=c("#1b9e77", "#d95f02", "#7570b3", "dark grey")) + ggtitle("Colored by condition") + theme_bw()

# #ggsave(paste(figure_directory, "scatter_by_stim.pdf"), width = 8, height = 7, useDingbats=FALSE)

Here’s for Unstim only:

plot_p_v_up(dfs = list("Unstim" = Unstim_df), sampleType = sampleType, paired_output = list("Unstim" = paired_output$Unstim), unpaired_output = list("Unstim" = unpaired_output$Unstim))

##  [1] "Unstim.Intermediate_monocytes_STAT1"   
##  [2] "Unstim.Naive_CD4_T_cells_IkB"          
##  [3] "Unstim.Intermediate_monocytes_STAT5"   
##  [4] "Unstim.CD4_T_cells_IkB"                
##  [5] "Unstim.pDCs_NFkB"                      
##  [6] "Unstim.CD4_T_cells_STAT1"              
##  [7] "Unstim.Naive_CD4_T_cells_STAT1"        
##  [8] "Unstim.Nonclassical_monocytes_STAT5"   
##  [9] "Unstim.Naive_CD8_T_cells_IkB"          
## [10] "Unstim.Nonclassical_monocytes_STAT1"   
## [11] "Unstim.Intermediate_monocytes_p38"     
## [12] "Unstim.Memory_CD4_T_cells_STAT1"       
## [13] "Unstim.Tregs_STAT1"                    
## [14] "Unstim.Intermediate_monocytes_MAPKAPK2"
## [15] "Unstim.Naive_CD4_T_cells_STAT5"        
## [16] "Unstim.CD4_T_cells_STAT5"              
## [17] "Unstim.Memory_CD4_T_cells_IkB"         
## [18] "Unstim.Memory_CD4_T_cells_STAT5"       
## [19] "Unstim.gd_T_cells_STAT1"               
## [20] "Unstim.Intermediate_monocytes_ERK"     
## [21] "Unstim.Naive_CD8_T_cells_STAT1"        
## [22] "Unstim.Nonclassical_monocytes_p38"     
## [23] "Unstim.Tregs_NFkB"                     
## [24] "Unstim.pDCs_MAPKAPK2"                  
## [25] "Unstim.Memory_CD4_T_cells_NFkB"        
## [26] "Unstim.Nonclassical_monocytes_IkB"     
## [27] "Unstim.Nonclassical_monocytes_MAPKAPK2"
## [28] "Unstim.cDCs_STAT5"                     
## [29] "Unstim.cDCs_STAT1"                     
## [30] "Unstim.CD56lo_NK_cells_STAT1"          
## [31] "Unstim.CD8_T_cells_STAT1"              
## [32] "Unstim.Tregs_STAT5"                    
## [33] "Unstim.pDCs_STAT1"                     
## [34] "Unstim.Classical_monocytes_STAT5"      
## [35] "Unstim.Classical_monocytes_STAT1"      
## [36] "Unstim.Nonclassical_monocytes_ERK"     
## [37] "Unstim.pDCs_p38"                       
## [38] "Unstim.Naive_CD8_T_cells_STAT5"        
## [39] "Unstim.Memory_CD8_T_cells_MAPKAPK2"    
## [40] "Unstim.B_cells_ERK"                    
## [41] "Unstim.Memory_CD4_T_cells_MAPKAPK2"    
## [42] "Unstim.Th1_T_cells_CREB"               
## [43] "Unstim.Th1_T_cells_S6"                 
## [44] "Unstim.Naive_CD8_T_cells_ERK"          
## [45] "Unstim.CD8_T_cells_ERK"                
## [46] "Unstim.Tregs_S6"                       
## [47] "Unstim.Th1_T_cells_MAPKAPK2"           
## [48] "Unstim.CD8_T_cells_MAPKAPK2"           
## [49] "Unstim.gd_T_cells_MAPKAPK2"            
## [50] "Unstim.B_cells_S6"                     
## [51] "Unstim.CD4_T_cells_MAPKAPK2"           
## [52] "Unstim.CD56lo_NK_cells_S6"             
## [53] "Unstim.Th1_T_cells_ERK"                
## [54] "Unstim.CD56hi_NK_cells_IkB"            
## [55] "Unstim.B_cells_NFkB"                   
## [56] "Unstim.Tregs_MAPKAPK2"                 
## [57] "Unstim.Memory_CD8_T_cells_ERK"         
## [58] "Unstim.CD56lo_NK_cells_CREB"           
## [59] "Unstim.B_cells_STAT5"                  
## [60] "Unstim.Naive_CD4_T_cells_MAPKAPK2"     
## [61] "Unstim.Naive_CD4_T_cells_ERK"          
## [62] "Unstim.Naive_CD8_T_cells_MAPKAPK2"     
## [63] "Unstim.Th1_T_cells_STAT3"              
## [64] "Unstim.B_cells_MAPKAPK2"               
## [65] "Unstim.CD56hi_NK_cells_MAPKAPK2"       
## [66] "Unstim.Tregs_CREB"                     
## [67] "Unstim.CD4_T_cells_S6"                 
## [68] "Unstim.CD4_T_cells_ERK"                
## [69] "Unstim.B_cells_CREB"                   
## [70] "Unstim.Naive_CD8_T_cells_CREB"         
## [71] "Unstim.Naive_CD4_T_cells_CREB"         
## [72] "Unstim.CD56hi_NK_cells_S6"             
## [73] "Unstim.Granulocytes_MAPKAPK2"          
## [74] "Unstim.CD56hi_NK_cells_ERK"            
## [75] "Unstim.Th1_T_cells_STAT5"              
## [76] "Unstim.CD56hi_NK_cells_CREB"           
## [77] "Unstim.Memory_CD4_T_cells_S6"          
## [78] "Unstim.Memory_CD4_T_cells_ERK"         
## [79] "Unstim.Memory_CD8_T_cells_STAT5"       
## [80] "Unstim.Th1_T_cells_IkB"                
## [81] "Unstim.Memory_CD4_T_cells_CREB"        
## [82] "Unstim.Memory_CD8_T_cells_IkB"         
## [83] "Unstim.CD4_T_cells_CREB"               
## [84] "Unstim.Naive_CD4_T_cells_S6"           
## [85] "Unstim.Granulocytes_CREB"              
## [86] "Unstim.CD56lo_NK_cells_IkB"            
## [87] "Unstim.Th1_T_cells_STAT1"              
## [88] "Unstim.MDSCs_CREB"                     
## [89] "Unstim.cDCs_CREB"                      
## [90] "Unstim.Nonclassical_monocytes_S6"      
##  [1] "Unstim.Intermediate_monocytes_STAT1"   
##  [2] "Unstim.Intermediate_monocytes_STAT5"   
##  [3] "Unstim.Naive_CD4_T_cells_STAT5"        
##  [4] "Unstim.CD4_T_cells_STAT5"              
##  [5] "Unstim.pDCs_NFkB"                      
##  [6] "Unstim.Memory_CD4_T_cells_STAT5"       
##  [7] "Unstim.Naive_CD4_T_cells_IkB"          
##  [8] "Unstim.Intermediate_monocytes_ERK"     
##  [9] "Unstim.pDCs_STAT1"                     
## [10] "Unstim.Nonclassical_monocytes_STAT1"   
## [11] "Unstim.Intermediate_monocytes_p38"     
## [12] "Unstim.Tregs_STAT1"                    
## [13] "Unstim.cDCs_STAT5"                     
## [14] "Unstim.CD4_T_cells_STAT1"              
## [15] "Unstim.Naive_CD4_T_cells_STAT1"        
## [16] "Unstim.Classical_monocytes_STAT5"      
## [17] "Unstim.gd_T_cells_STAT1"               
## [18] "Unstim.Nonclassical_monocytes_STAT5"   
## [19] "Unstim.Memory_CD4_T_cells_STAT1"       
## [20] "Unstim.Intermediate_monocytes_MAPKAPK2"
## [21] "Unstim.Naive_CD8_T_cells_IkB"          
## [22] "Unstim.cDCs_STAT1"                     
## [23] "Unstim.CD4_T_cells_IkB"                
## [24] "Unstim.Nonclassical_monocytes_p38"     
## [25] "Unstim.Classical_monocytes_STAT1"      
## [26] "Unstim.Naive_CD8_T_cells_STAT1"        
## [27] "Unstim.Tregs_STAT5"                    
## [28] "Unstim.pDCs_p38"                       
## [29] "Unstim.Naive_CD8_T_cells_STAT5"        
## [30] "Unstim.CD56lo_NK_cells_STAT1"          
## [31] "Unstim.Tregs_NFkB"                     
## [32] "Unstim.B_cells_ERK"                    
## [33] "Unstim.Th1_T_cells_CREB"               
## [34] "Unstim.Memory_CD8_T_cells_MAPKAPK2"    
## [35] "Unstim.CD56lo_NK_cells_CREB"           
## [36] "Unstim.CD8_T_cells_ERK"                
## [37] "Unstim.Naive_CD8_T_cells_ERK"          
## [38] "Unstim.Th1_T_cells_S6"                 
## [39] "Unstim.Th1_T_cells_MAPKAPK2"           
## [40] "Unstim.Th1_T_cells_ERK"                
## [41] "Unstim.B_cells_S6"                     
## [42] "Unstim.Memory_CD8_T_cells_ERK"         
## [43] "Unstim.gd_T_cells_MAPKAPK2"            
## [44] "Unstim.CD8_T_cells_MAPKAPK2"           
## [45] "Unstim.Naive_CD4_T_cells_ERK"          
## [46] "Unstim.CD56hi_NK_cells_CREB"           
## [47] "Unstim.B_cells_CREB"                   
## [48] "Unstim.Th1_T_cells_STAT3"              
## [49] "Unstim.Memory_CD4_T_cells_MAPKAPK2"    
## [50] "Unstim.CD56lo_NK_cells_S6"             
## [51] "Unstim.Tregs_S6"                       
## [52] "Unstim.Tregs_CREB"                     
## [53] "Unstim.Naive_CD8_T_cells_CREB"         
## [54] "Unstim.CD4_T_cells_ERK"                
## [55] "Unstim.Granulocytes_MAPKAPK2"          
## [56] "Unstim.CD56hi_NK_cells_IkB"            
## [57] "Unstim.B_cells_NFkB"                   
## [58] "Unstim.B_cells_STAT5"                  
## [59] "Unstim.Naive_CD4_T_cells_CREB"         
## [60] "Unstim.Th1_T_cells_STAT5"              
## [61] "Unstim.CD56hi_NK_cells_ERK"            
## [62] "Unstim.MDSCs_CREB"                     
## [63] "Unstim.B_cells_MAPKAPK2"               
## [64] "Unstim.Granulocytes_CREB"              
## [65] "Unstim.CD4_T_cells_MAPKAPK2"           
## [66] "Unstim.Memory_CD4_T_cells_ERK"         
## [67] "Unstim.Tregs_MAPKAPK2"                 
## [68] "Unstim.CD56hi_NK_cells_MAPKAPK2"       
## [69] "Unstim.Naive_CD8_T_cells_MAPKAPK2"     
## [70] "Unstim.cDCs_CREB"                      
## [71] "Unstim.Th1_T_cells_IkB"                
## [72] "Unstim.CD56hi_NK_cells_S6"             
## [73] "Unstim.Memory_CD4_T_cells_CREB"        
## [74] "Unstim.Memory_CD8_T_cells_STAT5"       
##   [1]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [12] FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE
##  [23] FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE
##  [34]  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE
##  [45] FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE
##  [56] FALSE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE
##  [67]  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE
##  [78] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE
##  [89] FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE
## [100] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE
## [111]  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE
## [122]  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [144]  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE
## [155] FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [166]  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE
## [177]  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE
## [188]  TRUE  TRUE  TRUE
##   [1]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [12] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE
##  [23] FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE
##  [34]  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE
##  [45] FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE
##  [56] FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE
##  [67]  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE
##  [78] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE
##  [89] FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE
## [100] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE
## [111]  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE
## [122]  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [144]  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE
## [155] FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [166]  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE
## [177]  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE
## [188] FALSE FALSE  TRUE

##                                        unpaired_pvals paired_pvals
## Unstim.Granulocytes_CREB                 1.454526e-02 1.766102e-02
## Unstim.Granulocytes_STAT5                3.202311e-01 3.277756e-01
## Unstim.Granulocytes_p38                  1.245449e-01 8.248464e-02
## Unstim.Granulocytes_STAT1                6.426266e-01 5.630320e-01
## Unstim.Granulocytes_STAT3                4.620542e-01 4.622732e-01
## Unstim.Granulocytes_S6                   6.413594e-01 4.921344e-01
## Unstim.Granulocytes_MAPKAPK2             2.772374e-03 2.676850e-03
## Unstim.Granulocytes_IkB                  8.217323e-01 7.689908e-01
## Unstim.Granulocytes_NFkB                 2.655910e-02 9.547049e-02
## Unstim.Granulocytes_ERK                  6.914283e-01 6.393495e-01
## Unstim.CD8_T_cells_CREB                  1.361972e-01 7.578972e-02
## Unstim.CD8_T_cells_STAT5                 4.693152e-01 4.209354e-01
## Unstim.CD8_T_cells_p38                   4.062352e-01 6.141304e-02
## Unstim.CD8_T_cells_STAT1                 1.215706e-02 3.715064e-04
## Unstim.CD8_T_cells_STAT3                 9.809138e-01 9.777724e-01
## Unstim.CD8_T_cells_S6                    2.556543e-01 4.064876e-02
## Unstim.CD8_T_cells_MAPKAPK2              6.549684e-04 5.489678e-06
## Unstim.CD8_T_cells_IkB                   6.203808e-01 4.167615e-01
## Unstim.CD8_T_cells_NFkB                  3.241919e-01 1.012624e-02
## Unstim.CD8_T_cells_ERK                   1.576608e-06 1.597554e-06
## Unstim.CD4_T_cells_CREB                  1.026805e-02 5.247107e-03
## Unstim.CD4_T_cells_STAT5                 2.590401e-04 4.102107e-04
## Unstim.CD4_T_cells_p38                   7.276975e-02 4.219835e-03
## Unstim.CD4_T_cells_STAT1                 3.579931e-04 2.324301e-05
## Unstim.CD4_T_cells_STAT3                 3.697803e-01 3.395004e-01
## Unstim.CD4_T_cells_S6                    2.311343e-02 1.194707e-04
## Unstim.CD4_T_cells_MAPKAPK2              1.232085e-02 8.268912e-07
## Unstim.CD4_T_cells_IkB                   5.646785e-03 4.741550e-06
## Unstim.CD4_T_cells_NFkB                  1.883986e-01 1.734440e-02
## Unstim.CD4_T_cells_ERK                   1.718611e-03 6.638037e-04
## Unstim.Naive_CD4_T_cells_CREB            8.010365e-04 5.605928e-04
## Unstim.Naive_CD4_T_cells_STAT5           2.348562e-04 3.773025e-04
## Unstim.Naive_CD4_T_cells_p38             1.507699e-01 1.574535e-02
## Unstim.Naive_CD4_T_cells_STAT1           4.646169e-04 3.322016e-05
## Unstim.Naive_CD4_T_cells_STAT3           7.089910e-01 6.845043e-01
## Unstim.Naive_CD4_T_cells_S6              1.388757e-01 3.476053e-03
## Unstim.Naive_CD4_T_cells_MAPKAPK2        6.786987e-02 5.914279e-06
## Unstim.Naive_CD4_T_cells_IkB             6.495783e-04 7.691806e-07
## Unstim.Naive_CD4_T_cells_NFkB            8.945786e-01 7.670955e-01
## Unstim.Naive_CD4_T_cells_ERK             2.342420e-04 7.289549e-05
## Unstim.Naive_CD8_T_cells_CREB            1.645490e-03 1.348310e-03
## Unstim.Naive_CD8_T_cells_STAT5           9.294308e-03 8.910078e-03
## Unstim.Naive_CD8_T_cells_p38             2.050132e-01 1.702127e-02
## Unstim.Naive_CD8_T_cells_STAT1           1.345853e-03 8.396036e-05
## Unstim.Naive_CD8_T_cells_STAT3           3.428543e-01 3.008317e-01
## Unstim.Naive_CD8_T_cells_S6              3.548405e-01 3.966789e-02
## Unstim.Naive_CD8_T_cells_MAPKAPK2        1.887013e-02 5.267062e-05
## Unstim.Naive_CD8_T_cells_IkB             3.719079e-03 8.364752e-05
## Unstim.Naive_CD8_T_cells_NFkB            3.113698e-01 7.074941e-03
## Unstim.Naive_CD8_T_cells_ERK             1.108382e-06 1.140432e-06
## Unstim.Memory_CD8_T_cells_CREB           7.124438e-02 8.493809e-02
## Unstim.Memory_CD8_T_cells_STAT5          7.766084e-03 1.107976e-03
## Unstim.Memory_CD8_T_cells_p38            8.608828e-01 6.248965e-01
## Unstim.Memory_CD8_T_cells_STAT1          3.000903e-01 6.019463e-02
## Unstim.Memory_CD8_T_cells_STAT3          2.329910e-01 8.151749e-02
## Unstim.Memory_CD8_T_cells_S6             5.015557e-01 3.766946e-01
## Unstim.Memory_CD8_T_cells_MAPKAPK2       4.289447e-08 3.197727e-09
## Unstim.Memory_CD8_T_cells_IkB            7.489677e-02 4.747219e-03
## Unstim.Memory_CD8_T_cells_NFkB           1.902935e-01 1.361559e-02
## Unstim.Memory_CD8_T_cells_ERK            7.326216e-05 9.539203e-05
## Unstim.B_cells_CREB                      4.699529e-04 1.488296e-03
## Unstim.B_cells_STAT5                     4.282646e-04 3.213624e-06
## Unstim.B_cells_p38                       8.608881e-01 7.707381e-01
## Unstim.B_cells_STAT1                     1.420030e-01 1.325136e-02
## Unstim.B_cells_STAT3                     1.314229e-01 3.268618e-03
## Unstim.B_cells_S6                        1.374829e-04 2.028772e-05
## Unstim.B_cells_MAPKAPK2                  6.119177e-03 8.396951e-05
## Unstim.B_cells_IkB                       3.808809e-01 3.084587e-01
## Unstim.B_cells_NFkB                      2.394253e-03 1.169341e-05
## Unstim.B_cells_ERK                       2.394424e-10 7.661840e-09
## Unstim.Classical_monocytes_CREB          4.871372e-02 4.378973e-02
## Unstim.Classical_monocytes_STAT5         8.686032e-05 1.776084e-03
## Unstim.Classical_monocytes_p38           8.929760e-01 8.865349e-01
## Unstim.Classical_monocytes_STAT1         7.685218e-03 5.132992e-03
## Unstim.Classical_monocytes_STAT3         9.648935e-01 9.616188e-01
## Unstim.Classical_monocytes_S6            1.916912e-01 1.977249e-01
## Unstim.Classical_monocytes_MAPKAPK2      7.545863e-01 7.423764e-01
## Unstim.Classical_monocytes_IkB           2.488134e-01 1.626920e-01
## Unstim.Classical_monocytes_NFkB          8.359534e-01 8.042830e-01
## Unstim.Classical_monocytes_ERK           9.070471e-01 9.106081e-01
## Unstim.Nonclassical_monocytes_CREB       9.999437e-01 9.998882e-01
## Unstim.Nonclassical_monocytes_STAT5      2.500545e-03 8.649429e-05
## Unstim.Nonclassical_monocytes_p38        1.176526e-02 8.956742e-04
## Unstim.Nonclassical_monocytes_STAT1      3.540195e-03 3.854479e-04
## Unstim.Nonclassical_monocytes_STAT3      9.774740e-01 9.775543e-01
## Unstim.Nonclassical_monocytes_S6         1.201234e-01 1.970360e-02
## Unstim.Nonclassical_monocytes_MAPKAPK2   7.928352e-02 3.283031e-03
## Unstim.Nonclassical_monocytes_IkB        6.181633e-02 1.287460e-04
## Unstim.Nonclassical_monocytes_NFkB       2.223616e-01 8.091316e-02
## Unstim.Nonclassical_monocytes_ERK        8.497462e-02 1.099825e-02
## Unstim.cDCs_CREB                         2.978829e-02 2.534888e-02
## Unstim.cDCs_STAT5                        4.570719e-05 9.560468e-04
## Unstim.cDCs_p38                          9.295080e-01 9.233575e-01
## Unstim.cDCs_STAT1                        4.520671e-03 2.810899e-03
## Unstim.cDCs_STAT3                        9.040712e-01 8.905688e-01
## Unstim.cDCs_S6                           1.382516e-01 1.463724e-01
## Unstim.cDCs_MAPKAPK2                     7.155604e-01 6.967120e-01
## Unstim.cDCs_IkB                          7.160396e-01 5.943869e-01
## Unstim.cDCs_NFkB                         8.253854e-01 7.951046e-01
## Unstim.cDCs_ERK                          9.791583e-01 9.795998e-01
## Unstim.pDCs_CREB                         1.680440e-01 7.024380e-02
## Unstim.pDCs_STAT5                        8.745327e-03 3.705902e-02
## Unstim.pDCs_p38                          4.055557e-03 3.329537e-03
## Unstim.pDCs_STAT1                        1.019619e-03 5.428900e-03
## Unstim.pDCs_STAT3                        9.602168e-01 9.570234e-01
## Unstim.pDCs_S6                           9.781401e-01 9.597474e-01
## Unstim.pDCs_MAPKAPK2                     3.577841e-02 4.503037e-05
## Unstim.pDCs_IkB                          6.299101e-01 4.837252e-01
## Unstim.pDCs_NFkB                         3.658271e-05 5.361157e-05
## Unstim.pDCs_ERK                          2.813664e-01 2.307529e-01
## Unstim.Th1_T_cells_CREB                  1.622506e-08 1.187629e-06
## Unstim.Th1_T_cells_STAT5                 4.187996e-03 2.254899e-03
## Unstim.Th1_T_cells_p38                   1.078065e-01 1.928383e-02
## Unstim.Th1_T_cells_STAT1                 4.591208e-02 7.466226e-03
## Unstim.Th1_T_cells_STAT3                 9.047198e-04 2.984681e-04
## Unstim.Th1_T_cells_S6                    2.243662e-06 6.166400e-07
## Unstim.Th1_T_cells_MAPKAPK2              1.064577e-05 7.758919e-06
## Unstim.Th1_T_cells_IkB                   2.656847e-02 5.335171e-03
## Unstim.Th1_T_cells_NFkB                  4.380637e-01 3.406712e-01
## Unstim.Th1_T_cells_ERK                   1.036898e-05 3.982343e-05
## Unstim.Intermediate_monocytes_CREB       2.368477e-01 6.276065e-02
## Unstim.Intermediate_monocytes_STAT5      1.708067e-06 1.013132e-06
## Unstim.Intermediate_monocytes_p38        1.536889e-03 1.901202e-04
## Unstim.Intermediate_monocytes_STAT1      6.182054e-07 4.919566e-07
## Unstim.Intermediate_monocytes_STAT3      6.530164e-01 6.034361e-01
## Unstim.Intermediate_monocytes_S6         8.796489e-01 8.056760e-01
## Unstim.Intermediate_monocytes_MAPKAPK2   5.797078e-03 2.812815e-04
## Unstim.Intermediate_monocytes_IkB        9.079383e-01 8.633441e-01
## Unstim.Intermediate_monocytes_NFkB       4.131249e-01 3.222873e-01
## Unstim.Intermediate_monocytes_ERK        3.400942e-03 1.063070e-03
## Unstim.MDSCs_CREB                        1.431711e-02 2.406331e-02
## Unstim.MDSCs_STAT5                       1.004589e-01 1.440341e-01
## Unstim.MDSCs_p38                         9.262632e-01 9.291324e-01
## Unstim.MDSCs_STAT1                       2.173736e-01 2.216592e-01
## Unstim.MDSCs_STAT3                       4.273799e-01 4.050715e-01
## Unstim.MDSCs_S6                          2.233628e-01 2.810726e-01
## Unstim.MDSCs_MAPKAPK2                    1.063303e-01 1.174360e-01
## Unstim.MDSCs_IkB                         2.891704e-01 1.468705e-01
## Unstim.MDSCs_NFkB                        4.003107e-01 3.588322e-01
## Unstim.MDSCs_ERK                         1.608174e-01 2.325880e-01
## Unstim.Tregs_CREB                        1.849495e-04 2.831146e-04
## Unstim.Tregs_STAT5                       3.411355e-03 1.863819e-03
## Unstim.Tregs_p38                         1.429264e-01 4.069978e-02
## Unstim.Tregs_STAT1                       1.080640e-04 1.976221e-05
## Unstim.Tregs_STAT3                       4.669445e-01 4.346297e-01
## Unstim.Tregs_S6                          4.661775e-04 3.916383e-07
## Unstim.Tregs_MAPKAPK2                    7.297274e-03 4.975501e-06
## Unstim.Tregs_IkB                         1.507385e-01 4.291098e-03
## Unstim.Tregs_NFkB                        4.781831e-03 1.089386e-04
## Unstim.Tregs_ERK                         1.231384e-01 5.786449e-02
## Unstim.CD56lo_NK_cells_CREB              2.469892e-06 1.965991e-04
## Unstim.CD56lo_NK_cells_STAT5             6.110157e-01 3.612637e-01
## Unstim.CD56lo_NK_cells_p38               1.093914e-01 4.941500e-02
## Unstim.CD56lo_NK_cells_STAT1             2.126306e-03 6.077802e-04
## Unstim.CD56lo_NK_cells_STAT3             7.280944e-02 1.386118e-03
## Unstim.CD56lo_NK_cells_S6                9.564652e-04 2.142184e-05
## Unstim.CD56lo_NK_cells_MAPKAPK2          2.854836e-01 2.691145e-02
## Unstim.CD56lo_NK_cells_IkB               4.065633e-02 4.839771e-03
## Unstim.CD56lo_NK_cells_NFkB              1.381510e-01 7.265945e-03
## Unstim.CD56lo_NK_cells_ERK               9.281219e-01 8.799194e-01
## Unstim.CD56hi_NK_cells_CREB              3.769450e-04 4.512660e-03
## Unstim.CD56hi_NK_cells_STAT5             2.902737e-01 1.693072e-01
## Unstim.CD56hi_NK_cells_p38               1.181669e-01 5.827460e-02
## Unstim.CD56hi_NK_cells_STAT1             9.078685e-03 1.343663e-02
## Unstim.CD56hi_NK_cells_STAT3             1.191327e-01 1.375071e-02
## Unstim.CD56hi_NK_cells_S6                2.178416e-02 1.711371e-03
## Unstim.CD56hi_NK_cells_MAPKAPK2          8.924476e-03 9.382232e-05
## Unstim.CD56hi_NK_cells_IkB               1.289271e-03 4.341278e-06
## Unstim.CD56hi_NK_cells_NFkB              4.803780e-02 2.360860e-02
## Unstim.CD56hi_NK_cells_ERK               3.493981e-03 1.853259e-03
## Unstim.gd_T_cells_CREB                   2.792406e-01 3.672940e-01
## Unstim.gd_T_cells_STAT5                  4.426911e-01 2.023715e-01
## Unstim.gd_T_cells_p38                    3.108195e-02 9.858180e-04
## Unstim.gd_T_cells_STAT1                  2.581577e-04 1.032419e-04
## Unstim.gd_T_cells_STAT3                  5.905688e-01 3.602265e-01
## Unstim.gd_T_cells_S6                     1.399920e-01 9.248786e-02
## Unstim.gd_T_cells_MAPKAPK2               1.276031e-04 2.605004e-06
## Unstim.gd_T_cells_IkB                    8.358901e-01 8.083248e-01
## Unstim.gd_T_cells_NFkB                   1.187126e-01 2.525241e-02
## Unstim.gd_T_cells_ERK                    4.172333e-01 3.931471e-01
## Unstim.Memory_CD4_T_cells_CREB           9.327271e-03 3.514399e-03
## Unstim.Memory_CD4_T_cells_STAT5          3.419699e-04 3.839441e-04
## Unstim.Memory_CD4_T_cells_p38            4.586416e-02 1.075034e-03
## Unstim.Memory_CD4_T_cells_STAT1          6.122297e-04 2.640403e-05
## Unstim.Memory_CD4_T_cells_STAT3          1.496695e-01 1.265940e-01
## Unstim.Memory_CD4_T_cells_S6             1.399293e-02 7.575542e-04
## Unstim.Memory_CD4_T_cells_MAPKAPK2       6.188081e-04 2.574874e-08
## Unstim.Memory_CD4_T_cells_IkB            3.240368e-02 6.630191e-05
## Unstim.Memory_CD4_T_cells_NFkB           2.572740e-02 1.015704e-04
## Unstim.Memory_CD4_T_cells_ERK            6.959549e-03 2.236756e-03
##                                        Significance_Bonferroni
## Unstim.Granulocytes_CREB                       Not significant
## Unstim.Granulocytes_STAT5                      Not significant
## Unstim.Granulocytes_p38                        Not significant
## Unstim.Granulocytes_STAT1                      Not significant
## Unstim.Granulocytes_STAT3                      Not significant
## Unstim.Granulocytes_S6                         Not significant
## Unstim.Granulocytes_MAPKAPK2                   Not significant
## Unstim.Granulocytes_IkB                        Not significant
## Unstim.Granulocytes_NFkB                       Not significant
## Unstim.Granulocytes_ERK                        Not significant
## Unstim.CD8_T_cells_CREB                        Not significant
## Unstim.CD8_T_cells_STAT5                       Not significant
## Unstim.CD8_T_cells_p38                         Not significant
## Unstim.CD8_T_cells_STAT1                       Not significant
## Unstim.CD8_T_cells_STAT3                       Not significant
## Unstim.CD8_T_cells_S6                          Not significant
## Unstim.CD8_T_cells_MAPKAPK2                        Paired only
## Unstim.CD8_T_cells_IkB                         Not significant
## Unstim.CD8_T_cells_NFkB                        Not significant
## Unstim.CD8_T_cells_ERK                                    Both
## Unstim.CD4_T_cells_CREB                        Not significant
## Unstim.CD4_T_cells_STAT5                         Unpaired only
## Unstim.CD4_T_cells_p38                         Not significant
## Unstim.CD4_T_cells_STAT1                           Paired only
## Unstim.CD4_T_cells_STAT3                       Not significant
## Unstim.CD4_T_cells_S6                              Paired only
## Unstim.CD4_T_cells_MAPKAPK2                        Paired only
## Unstim.CD4_T_cells_IkB                             Paired only
## Unstim.CD4_T_cells_NFkB                        Not significant
## Unstim.CD4_T_cells_ERK                         Not significant
## Unstim.Naive_CD4_T_cells_CREB                  Not significant
## Unstim.Naive_CD4_T_cells_STAT5                   Unpaired only
## Unstim.Naive_CD4_T_cells_p38                   Not significant
## Unstim.Naive_CD4_T_cells_STAT1                     Paired only
## Unstim.Naive_CD4_T_cells_STAT3                 Not significant
## Unstim.Naive_CD4_T_cells_S6                    Not significant
## Unstim.Naive_CD4_T_cells_MAPKAPK2                  Paired only
## Unstim.Naive_CD4_T_cells_IkB                       Paired only
## Unstim.Naive_CD4_T_cells_NFkB                  Not significant
## Unstim.Naive_CD4_T_cells_ERK                              Both
## Unstim.Naive_CD8_T_cells_CREB                  Not significant
## Unstim.Naive_CD8_T_cells_STAT5                 Not significant
## Unstim.Naive_CD8_T_cells_p38                   Not significant
## Unstim.Naive_CD8_T_cells_STAT1                     Paired only
## Unstim.Naive_CD8_T_cells_STAT3                 Not significant
## Unstim.Naive_CD8_T_cells_S6                    Not significant
## Unstim.Naive_CD8_T_cells_MAPKAPK2                  Paired only
## Unstim.Naive_CD8_T_cells_IkB                       Paired only
## Unstim.Naive_CD8_T_cells_NFkB                  Not significant
## Unstim.Naive_CD8_T_cells_ERK                              Both
## Unstim.Memory_CD8_T_cells_CREB                 Not significant
## Unstim.Memory_CD8_T_cells_STAT5                Not significant
## Unstim.Memory_CD8_T_cells_p38                  Not significant
## Unstim.Memory_CD8_T_cells_STAT1                Not significant
## Unstim.Memory_CD8_T_cells_STAT3                Not significant
## Unstim.Memory_CD8_T_cells_S6                   Not significant
## Unstim.Memory_CD8_T_cells_MAPKAPK2                        Both
## Unstim.Memory_CD8_T_cells_IkB                  Not significant
## Unstim.Memory_CD8_T_cells_NFkB                 Not significant
## Unstim.Memory_CD8_T_cells_ERK                             Both
## Unstim.B_cells_CREB                            Not significant
## Unstim.B_cells_STAT5                               Paired only
## Unstim.B_cells_p38                             Not significant
## Unstim.B_cells_STAT1                           Not significant
## Unstim.B_cells_STAT3                           Not significant
## Unstim.B_cells_S6                                         Both
## Unstim.B_cells_MAPKAPK2                            Paired only
## Unstim.B_cells_IkB                             Not significant
## Unstim.B_cells_NFkB                                Paired only
## Unstim.B_cells_ERK                                        Both
## Unstim.Classical_monocytes_CREB                Not significant
## Unstim.Classical_monocytes_STAT5                 Unpaired only
## Unstim.Classical_monocytes_p38                 Not significant
## Unstim.Classical_monocytes_STAT1               Not significant
## Unstim.Classical_monocytes_STAT3               Not significant
## Unstim.Classical_monocytes_S6                  Not significant
## Unstim.Classical_monocytes_MAPKAPK2            Not significant
## Unstim.Classical_monocytes_IkB                 Not significant
## Unstim.Classical_monocytes_NFkB                Not significant
## Unstim.Classical_monocytes_ERK                 Not significant
## Unstim.Nonclassical_monocytes_CREB             Not significant
## Unstim.Nonclassical_monocytes_STAT5                Paired only
## Unstim.Nonclassical_monocytes_p38              Not significant
## Unstim.Nonclassical_monocytes_STAT1            Not significant
## Unstim.Nonclassical_monocytes_STAT3            Not significant
## Unstim.Nonclassical_monocytes_S6               Not significant
## Unstim.Nonclassical_monocytes_MAPKAPK2         Not significant
## Unstim.Nonclassical_monocytes_IkB                  Paired only
## Unstim.Nonclassical_monocytes_NFkB             Not significant
## Unstim.Nonclassical_monocytes_ERK              Not significant
## Unstim.cDCs_CREB                               Not significant
## Unstim.cDCs_STAT5                                Unpaired only
## Unstim.cDCs_p38                                Not significant
## Unstim.cDCs_STAT1                              Not significant
## Unstim.cDCs_STAT3                              Not significant
## Unstim.cDCs_S6                                 Not significant
## Unstim.cDCs_MAPKAPK2                           Not significant
## Unstim.cDCs_IkB                                Not significant
## Unstim.cDCs_NFkB                               Not significant
## Unstim.cDCs_ERK                                Not significant
## Unstim.pDCs_CREB                               Not significant
## Unstim.pDCs_STAT5                              Not significant
## Unstim.pDCs_p38                                Not significant
## Unstim.pDCs_STAT1                              Not significant
## Unstim.pDCs_STAT3                              Not significant
## Unstim.pDCs_S6                                 Not significant
## Unstim.pDCs_MAPKAPK2                               Paired only
## Unstim.pDCs_IkB                                Not significant
## Unstim.pDCs_NFkB                                          Both
## Unstim.pDCs_ERK                                Not significant
## Unstim.Th1_T_cells_CREB                                   Both
## Unstim.Th1_T_cells_STAT5                       Not significant
## Unstim.Th1_T_cells_p38                         Not significant
## Unstim.Th1_T_cells_STAT1                       Not significant
## Unstim.Th1_T_cells_STAT3                       Not significant
## Unstim.Th1_T_cells_S6                                     Both
## Unstim.Th1_T_cells_MAPKAPK2                               Both
## Unstim.Th1_T_cells_IkB                         Not significant
## Unstim.Th1_T_cells_NFkB                        Not significant
## Unstim.Th1_T_cells_ERK                                    Both
## Unstim.Intermediate_monocytes_CREB             Not significant
## Unstim.Intermediate_monocytes_STAT5                       Both
## Unstim.Intermediate_monocytes_p38                  Paired only
## Unstim.Intermediate_monocytes_STAT1                       Both
## Unstim.Intermediate_monocytes_STAT3            Not significant
## Unstim.Intermediate_monocytes_S6               Not significant
## Unstim.Intermediate_monocytes_MAPKAPK2         Not significant
## Unstim.Intermediate_monocytes_IkB              Not significant
## Unstim.Intermediate_monocytes_NFkB             Not significant
## Unstim.Intermediate_monocytes_ERK              Not significant
## Unstim.MDSCs_CREB                              Not significant
## Unstim.MDSCs_STAT5                             Not significant
## Unstim.MDSCs_p38                               Not significant
## Unstim.MDSCs_STAT1                             Not significant
## Unstim.MDSCs_STAT3                             Not significant
## Unstim.MDSCs_S6                                Not significant
## Unstim.MDSCs_MAPKAPK2                          Not significant
## Unstim.MDSCs_IkB                               Not significant
## Unstim.MDSCs_NFkB                              Not significant
## Unstim.MDSCs_ERK                               Not significant
## Unstim.Tregs_CREB                                Unpaired only
## Unstim.Tregs_STAT5                             Not significant
## Unstim.Tregs_p38                               Not significant
## Unstim.Tregs_STAT1                                        Both
## Unstim.Tregs_STAT3                             Not significant
## Unstim.Tregs_S6                                    Paired only
## Unstim.Tregs_MAPKAPK2                              Paired only
## Unstim.Tregs_IkB                               Not significant
## Unstim.Tregs_NFkB                                  Paired only
## Unstim.Tregs_ERK                               Not significant
## Unstim.CD56lo_NK_cells_CREB                               Both
## Unstim.CD56lo_NK_cells_STAT5                   Not significant
## Unstim.CD56lo_NK_cells_p38                     Not significant
## Unstim.CD56lo_NK_cells_STAT1                   Not significant
## Unstim.CD56lo_NK_cells_STAT3                   Not significant
## Unstim.CD56lo_NK_cells_S6                          Paired only
## Unstim.CD56lo_NK_cells_MAPKAPK2                Not significant
## Unstim.CD56lo_NK_cells_IkB                     Not significant
## Unstim.CD56lo_NK_cells_NFkB                    Not significant
## Unstim.CD56lo_NK_cells_ERK                     Not significant
## Unstim.CD56hi_NK_cells_CREB                    Not significant
## Unstim.CD56hi_NK_cells_STAT5                   Not significant
## Unstim.CD56hi_NK_cells_p38                     Not significant
## Unstim.CD56hi_NK_cells_STAT1                   Not significant
## Unstim.CD56hi_NK_cells_STAT3                   Not significant
## Unstim.CD56hi_NK_cells_S6                      Not significant
## Unstim.CD56hi_NK_cells_MAPKAPK2                    Paired only
## Unstim.CD56hi_NK_cells_IkB                         Paired only
## Unstim.CD56hi_NK_cells_NFkB                    Not significant
## Unstim.CD56hi_NK_cells_ERK                     Not significant
## Unstim.gd_T_cells_CREB                         Not significant
## Unstim.gd_T_cells_STAT5                        Not significant
## Unstim.gd_T_cells_p38                          Not significant
## Unstim.gd_T_cells_STAT1                                   Both
## Unstim.gd_T_cells_STAT3                        Not significant
## Unstim.gd_T_cells_S6                           Not significant
## Unstim.gd_T_cells_MAPKAPK2                                Both
## Unstim.gd_T_cells_IkB                          Not significant
## Unstim.gd_T_cells_NFkB                         Not significant
## Unstim.gd_T_cells_ERK                          Not significant
## Unstim.Memory_CD4_T_cells_CREB                 Not significant
## Unstim.Memory_CD4_T_cells_STAT5                Not significant
## Unstim.Memory_CD4_T_cells_p38                  Not significant
## Unstim.Memory_CD4_T_cells_STAT1                    Paired only
## Unstim.Memory_CD4_T_cells_STAT3                Not significant
## Unstim.Memory_CD4_T_cells_S6                   Not significant
## Unstim.Memory_CD4_T_cells_MAPKAPK2                 Paired only
## Unstim.Memory_CD4_T_cells_IkB                      Paired only
## Unstim.Memory_CD4_T_cells_NFkB                     Paired only
## Unstim.Memory_CD4_T_cells_ERK                  Not significant
##                                        Significance_SAM
## Unstim.Granulocytes_CREB                           Both
## Unstim.Granulocytes_STAT5               Not significant
## Unstim.Granulocytes_p38                 Not significant
## Unstim.Granulocytes_STAT1               Not significant
## Unstim.Granulocytes_STAT3               Not significant
## Unstim.Granulocytes_S6                  Not significant
## Unstim.Granulocytes_MAPKAPK2                       Both
## Unstim.Granulocytes_IkB                 Not significant
## Unstim.Granulocytes_NFkB                Not significant
## Unstim.Granulocytes_ERK                 Not significant
## Unstim.CD8_T_cells_CREB                 Not significant
## Unstim.CD8_T_cells_STAT5                Not significant
## Unstim.CD8_T_cells_p38                  Not significant
## Unstim.CD8_T_cells_STAT1                    Paired only
## Unstim.CD8_T_cells_STAT3                Not significant
## Unstim.CD8_T_cells_S6                   Not significant
## Unstim.CD8_T_cells_MAPKAPK2                        Both
## Unstim.CD8_T_cells_IkB                  Not significant
## Unstim.CD8_T_cells_NFkB                 Not significant
## Unstim.CD8_T_cells_ERK                             Both
## Unstim.CD4_T_cells_CREB                     Paired only
## Unstim.CD4_T_cells_STAT5                           Both
## Unstim.CD4_T_cells_p38                  Not significant
## Unstim.CD4_T_cells_STAT1                           Both
## Unstim.CD4_T_cells_STAT3                Not significant
## Unstim.CD4_T_cells_S6                       Paired only
## Unstim.CD4_T_cells_MAPKAPK2                        Both
## Unstim.CD4_T_cells_IkB                             Both
## Unstim.CD4_T_cells_NFkB                 Not significant
## Unstim.CD4_T_cells_ERK                             Both
## Unstim.Naive_CD4_T_cells_CREB                      Both
## Unstim.Naive_CD4_T_cells_STAT5                     Both
## Unstim.Naive_CD4_T_cells_p38            Not significant
## Unstim.Naive_CD4_T_cells_STAT1                     Both
## Unstim.Naive_CD4_T_cells_STAT3          Not significant
## Unstim.Naive_CD4_T_cells_S6                 Paired only
## Unstim.Naive_CD4_T_cells_MAPKAPK2           Paired only
## Unstim.Naive_CD4_T_cells_IkB                       Both
## Unstim.Naive_CD4_T_cells_NFkB           Not significant
## Unstim.Naive_CD4_T_cells_ERK                       Both
## Unstim.Naive_CD8_T_cells_CREB                      Both
## Unstim.Naive_CD8_T_cells_STAT5                     Both
## Unstim.Naive_CD8_T_cells_p38            Not significant
## Unstim.Naive_CD8_T_cells_STAT1                     Both
## Unstim.Naive_CD8_T_cells_STAT3          Not significant
## Unstim.Naive_CD8_T_cells_S6             Not significant
## Unstim.Naive_CD8_T_cells_MAPKAPK2                  Both
## Unstim.Naive_CD8_T_cells_IkB                       Both
## Unstim.Naive_CD8_T_cells_NFkB           Not significant
## Unstim.Naive_CD8_T_cells_ERK                       Both
## Unstim.Memory_CD8_T_cells_CREB          Not significant
## Unstim.Memory_CD8_T_cells_STAT5                    Both
## Unstim.Memory_CD8_T_cells_p38           Not significant
## Unstim.Memory_CD8_T_cells_STAT1         Not significant
## Unstim.Memory_CD8_T_cells_STAT3         Not significant
## Unstim.Memory_CD8_T_cells_S6            Not significant
## Unstim.Memory_CD8_T_cells_MAPKAPK2                 Both
## Unstim.Memory_CD8_T_cells_IkB               Paired only
## Unstim.Memory_CD8_T_cells_NFkB          Not significant
## Unstim.Memory_CD8_T_cells_ERK                      Both
## Unstim.B_cells_CREB                                Both
## Unstim.B_cells_STAT5                               Both
## Unstim.B_cells_p38                      Not significant
## Unstim.B_cells_STAT1                    Not significant
## Unstim.B_cells_STAT3                    Not significant
## Unstim.B_cells_S6                                  Both
## Unstim.B_cells_MAPKAPK2                            Both
## Unstim.B_cells_IkB                      Not significant
## Unstim.B_cells_NFkB                                Both
## Unstim.B_cells_ERK                                 Both
## Unstim.Classical_monocytes_CREB         Not significant
## Unstim.Classical_monocytes_STAT5                   Both
## Unstim.Classical_monocytes_p38          Not significant
## Unstim.Classical_monocytes_STAT1                   Both
## Unstim.Classical_monocytes_STAT3        Not significant
## Unstim.Classical_monocytes_S6           Not significant
## Unstim.Classical_monocytes_MAPKAPK2     Not significant
## Unstim.Classical_monocytes_IkB          Not significant
## Unstim.Classical_monocytes_NFkB         Not significant
## Unstim.Classical_monocytes_ERK          Not significant
## Unstim.Nonclassical_monocytes_CREB      Not significant
## Unstim.Nonclassical_monocytes_STAT5                Both
## Unstim.Nonclassical_monocytes_p38                  Both
## Unstim.Nonclassical_monocytes_STAT1                Both
## Unstim.Nonclassical_monocytes_STAT3     Not significant
## Unstim.Nonclassical_monocytes_S6            Paired only
## Unstim.Nonclassical_monocytes_MAPKAPK2      Paired only
## Unstim.Nonclassical_monocytes_IkB           Paired only
## Unstim.Nonclassical_monocytes_NFkB      Not significant
## Unstim.Nonclassical_monocytes_ERK           Paired only
## Unstim.cDCs_CREB                                   Both
## Unstim.cDCs_STAT5                                  Both
## Unstim.cDCs_p38                         Not significant
## Unstim.cDCs_STAT1                                  Both
## Unstim.cDCs_STAT3                       Not significant
## Unstim.cDCs_S6                          Not significant
## Unstim.cDCs_MAPKAPK2                    Not significant
## Unstim.cDCs_IkB                         Not significant
## Unstim.cDCs_NFkB                        Not significant
## Unstim.cDCs_ERK                         Not significant
## Unstim.pDCs_CREB                        Not significant
## Unstim.pDCs_STAT5                       Not significant
## Unstim.pDCs_p38                                    Both
## Unstim.pDCs_STAT1                                  Both
## Unstim.pDCs_STAT3                       Not significant
## Unstim.pDCs_S6                          Not significant
## Unstim.pDCs_MAPKAPK2                        Paired only
## Unstim.pDCs_IkB                         Not significant
## Unstim.pDCs_NFkB                                   Both
## Unstim.pDCs_ERK                         Not significant
## Unstim.Th1_T_cells_CREB                            Both
## Unstim.Th1_T_cells_STAT5                           Both
## Unstim.Th1_T_cells_p38                  Not significant
## Unstim.Th1_T_cells_STAT1                    Paired only
## Unstim.Th1_T_cells_STAT3                           Both
## Unstim.Th1_T_cells_S6                              Both
## Unstim.Th1_T_cells_MAPKAPK2                        Both
## Unstim.Th1_T_cells_IkB                             Both
## Unstim.Th1_T_cells_NFkB                 Not significant
## Unstim.Th1_T_cells_ERK                             Both
## Unstim.Intermediate_monocytes_CREB      Not significant
## Unstim.Intermediate_monocytes_STAT5                Both
## Unstim.Intermediate_monocytes_p38                  Both
## Unstim.Intermediate_monocytes_STAT1                Both
## Unstim.Intermediate_monocytes_STAT3     Not significant
## Unstim.Intermediate_monocytes_S6        Not significant
## Unstim.Intermediate_monocytes_MAPKAPK2             Both
## Unstim.Intermediate_monocytes_IkB       Not significant
## Unstim.Intermediate_monocytes_NFkB      Not significant
## Unstim.Intermediate_monocytes_ERK                  Both
## Unstim.MDSCs_CREB                                  Both
## Unstim.MDSCs_STAT5                      Not significant
## Unstim.MDSCs_p38                        Not significant
## Unstim.MDSCs_STAT1                      Not significant
## Unstim.MDSCs_STAT3                      Not significant
## Unstim.MDSCs_S6                         Not significant
## Unstim.MDSCs_MAPKAPK2                   Not significant
## Unstim.MDSCs_IkB                        Not significant
## Unstim.MDSCs_NFkB                       Not significant
## Unstim.MDSCs_ERK                        Not significant
## Unstim.Tregs_CREB                                  Both
## Unstim.Tregs_STAT5                                 Both
## Unstim.Tregs_p38                        Not significant
## Unstim.Tregs_STAT1                                 Both
## Unstim.Tregs_STAT3                      Not significant
## Unstim.Tregs_S6                                    Both
## Unstim.Tregs_MAPKAPK2                              Both
## Unstim.Tregs_IkB                        Not significant
## Unstim.Tregs_NFkB                                  Both
## Unstim.Tregs_ERK                        Not significant
## Unstim.CD56lo_NK_cells_CREB                        Both
## Unstim.CD56lo_NK_cells_STAT5            Not significant
## Unstim.CD56lo_NK_cells_p38              Not significant
## Unstim.CD56lo_NK_cells_STAT1                       Both
## Unstim.CD56lo_NK_cells_STAT3            Not significant
## Unstim.CD56lo_NK_cells_S6                          Both
## Unstim.CD56lo_NK_cells_MAPKAPK2         Not significant
## Unstim.CD56lo_NK_cells_IkB                  Paired only
## Unstim.CD56lo_NK_cells_NFkB             Not significant
## Unstim.CD56lo_NK_cells_ERK              Not significant
## Unstim.CD56hi_NK_cells_CREB                        Both
## Unstim.CD56hi_NK_cells_STAT5            Not significant
## Unstim.CD56hi_NK_cells_p38              Not significant
## Unstim.CD56hi_NK_cells_STAT1            Not significant
## Unstim.CD56hi_NK_cells_STAT3            Not significant
## Unstim.CD56hi_NK_cells_S6                          Both
## Unstim.CD56hi_NK_cells_MAPKAPK2                    Both
## Unstim.CD56hi_NK_cells_IkB                         Both
## Unstim.CD56hi_NK_cells_NFkB             Not significant
## Unstim.CD56hi_NK_cells_ERK                         Both
## Unstim.gd_T_cells_CREB                  Not significant
## Unstim.gd_T_cells_STAT5                 Not significant
## Unstim.gd_T_cells_p38                   Not significant
## Unstim.gd_T_cells_STAT1                            Both
## Unstim.gd_T_cells_STAT3                 Not significant
## Unstim.gd_T_cells_S6                    Not significant
## Unstim.gd_T_cells_MAPKAPK2                         Both
## Unstim.gd_T_cells_IkB                   Not significant
## Unstim.gd_T_cells_NFkB                  Not significant
## Unstim.gd_T_cells_ERK                   Not significant
## Unstim.Memory_CD4_T_cells_CREB                     Both
## Unstim.Memory_CD4_T_cells_STAT5                    Both
## Unstim.Memory_CD4_T_cells_p38           Not significant
## Unstim.Memory_CD4_T_cells_STAT1                    Both
## Unstim.Memory_CD4_T_cells_STAT3         Not significant
## Unstim.Memory_CD4_T_cells_S6                Paired only
## Unstim.Memory_CD4_T_cells_MAPKAPK2                 Both
## Unstim.Memory_CD4_T_cells_IkB               Paired only
## Unstim.Memory_CD4_T_cells_NFkB              Paired only
## Unstim.Memory_CD4_T_cells_ERK                      Both
##                                                                      Features
## Unstim.Granulocytes_CREB                             Unstim.Granulocytes_CREB
## Unstim.Granulocytes_STAT5                           Unstim.Granulocytes_STAT5
## Unstim.Granulocytes_p38                               Unstim.Granulocytes_p38
## Unstim.Granulocytes_STAT1                           Unstim.Granulocytes_STAT1
## Unstim.Granulocytes_STAT3                           Unstim.Granulocytes_STAT3
## Unstim.Granulocytes_S6                                 Unstim.Granulocytes_S6
## Unstim.Granulocytes_MAPKAPK2                     Unstim.Granulocytes_MAPKAPK2
## Unstim.Granulocytes_IkB                               Unstim.Granulocytes_IkB
## Unstim.Granulocytes_NFkB                             Unstim.Granulocytes_NFkB
## Unstim.Granulocytes_ERK                               Unstim.Granulocytes_ERK
## Unstim.CD8_T_cells_CREB                               Unstim.CD8_T_cells_CREB
## Unstim.CD8_T_cells_STAT5                             Unstim.CD8_T_cells_STAT5
## Unstim.CD8_T_cells_p38                                 Unstim.CD8_T_cells_p38
## Unstim.CD8_T_cells_STAT1                             Unstim.CD8_T_cells_STAT1
## Unstim.CD8_T_cells_STAT3                             Unstim.CD8_T_cells_STAT3
## Unstim.CD8_T_cells_S6                                   Unstim.CD8_T_cells_S6
## Unstim.CD8_T_cells_MAPKAPK2                       Unstim.CD8_T_cells_MAPKAPK2
## Unstim.CD8_T_cells_IkB                                 Unstim.CD8_T_cells_IkB
## Unstim.CD8_T_cells_NFkB                               Unstim.CD8_T_cells_NFkB
## Unstim.CD8_T_cells_ERK                                 Unstim.CD8_T_cells_ERK
## Unstim.CD4_T_cells_CREB                               Unstim.CD4_T_cells_CREB
## Unstim.CD4_T_cells_STAT5                             Unstim.CD4_T_cells_STAT5
## Unstim.CD4_T_cells_p38                                 Unstim.CD4_T_cells_p38
## Unstim.CD4_T_cells_STAT1                             Unstim.CD4_T_cells_STAT1
## Unstim.CD4_T_cells_STAT3                             Unstim.CD4_T_cells_STAT3
## Unstim.CD4_T_cells_S6                                   Unstim.CD4_T_cells_S6
## Unstim.CD4_T_cells_MAPKAPK2                       Unstim.CD4_T_cells_MAPKAPK2
## Unstim.CD4_T_cells_IkB                                 Unstim.CD4_T_cells_IkB
## Unstim.CD4_T_cells_NFkB                               Unstim.CD4_T_cells_NFkB
## Unstim.CD4_T_cells_ERK                                 Unstim.CD4_T_cells_ERK
## Unstim.Naive_CD4_T_cells_CREB                   Unstim.Naive_CD4_T_cells_CREB
## Unstim.Naive_CD4_T_cells_STAT5                 Unstim.Naive_CD4_T_cells_STAT5
## Unstim.Naive_CD4_T_cells_p38                     Unstim.Naive_CD4_T_cells_p38
## Unstim.Naive_CD4_T_cells_STAT1                 Unstim.Naive_CD4_T_cells_STAT1
## Unstim.Naive_CD4_T_cells_STAT3                 Unstim.Naive_CD4_T_cells_STAT3
## Unstim.Naive_CD4_T_cells_S6                       Unstim.Naive_CD4_T_cells_S6
## Unstim.Naive_CD4_T_cells_MAPKAPK2           Unstim.Naive_CD4_T_cells_MAPKAPK2
## Unstim.Naive_CD4_T_cells_IkB                     Unstim.Naive_CD4_T_cells_IkB
## Unstim.Naive_CD4_T_cells_NFkB                   Unstim.Naive_CD4_T_cells_NFkB
## Unstim.Naive_CD4_T_cells_ERK                     Unstim.Naive_CD4_T_cells_ERK
## Unstim.Naive_CD8_T_cells_CREB                   Unstim.Naive_CD8_T_cells_CREB
## Unstim.Naive_CD8_T_cells_STAT5                 Unstim.Naive_CD8_T_cells_STAT5
## Unstim.Naive_CD8_T_cells_p38                     Unstim.Naive_CD8_T_cells_p38
## Unstim.Naive_CD8_T_cells_STAT1                 Unstim.Naive_CD8_T_cells_STAT1
## Unstim.Naive_CD8_T_cells_STAT3                 Unstim.Naive_CD8_T_cells_STAT3
## Unstim.Naive_CD8_T_cells_S6                       Unstim.Naive_CD8_T_cells_S6
## Unstim.Naive_CD8_T_cells_MAPKAPK2           Unstim.Naive_CD8_T_cells_MAPKAPK2
## Unstim.Naive_CD8_T_cells_IkB                     Unstim.Naive_CD8_T_cells_IkB
## Unstim.Naive_CD8_T_cells_NFkB                   Unstim.Naive_CD8_T_cells_NFkB
## Unstim.Naive_CD8_T_cells_ERK                     Unstim.Naive_CD8_T_cells_ERK
## Unstim.Memory_CD8_T_cells_CREB                 Unstim.Memory_CD8_T_cells_CREB
## Unstim.Memory_CD8_T_cells_STAT5               Unstim.Memory_CD8_T_cells_STAT5
## Unstim.Memory_CD8_T_cells_p38                   Unstim.Memory_CD8_T_cells_p38
## Unstim.Memory_CD8_T_cells_STAT1               Unstim.Memory_CD8_T_cells_STAT1
## Unstim.Memory_CD8_T_cells_STAT3               Unstim.Memory_CD8_T_cells_STAT3
## Unstim.Memory_CD8_T_cells_S6                     Unstim.Memory_CD8_T_cells_S6
## Unstim.Memory_CD8_T_cells_MAPKAPK2         Unstim.Memory_CD8_T_cells_MAPKAPK2
## Unstim.Memory_CD8_T_cells_IkB                   Unstim.Memory_CD8_T_cells_IkB
## Unstim.Memory_CD8_T_cells_NFkB                 Unstim.Memory_CD8_T_cells_NFkB
## Unstim.Memory_CD8_T_cells_ERK                   Unstim.Memory_CD8_T_cells_ERK
## Unstim.B_cells_CREB                                       Unstim.B_cells_CREB
## Unstim.B_cells_STAT5                                     Unstim.B_cells_STAT5
## Unstim.B_cells_p38                                         Unstim.B_cells_p38
## Unstim.B_cells_STAT1                                     Unstim.B_cells_STAT1
## Unstim.B_cells_STAT3                                     Unstim.B_cells_STAT3
## Unstim.B_cells_S6                                           Unstim.B_cells_S6
## Unstim.B_cells_MAPKAPK2                               Unstim.B_cells_MAPKAPK2
## Unstim.B_cells_IkB                                         Unstim.B_cells_IkB
## Unstim.B_cells_NFkB                                       Unstim.B_cells_NFkB
## Unstim.B_cells_ERK                                         Unstim.B_cells_ERK
## Unstim.Classical_monocytes_CREB               Unstim.Classical_monocytes_CREB
## Unstim.Classical_monocytes_STAT5             Unstim.Classical_monocytes_STAT5
## Unstim.Classical_monocytes_p38                 Unstim.Classical_monocytes_p38
## Unstim.Classical_monocytes_STAT1             Unstim.Classical_monocytes_STAT1
## Unstim.Classical_monocytes_STAT3             Unstim.Classical_monocytes_STAT3
## Unstim.Classical_monocytes_S6                   Unstim.Classical_monocytes_S6
## Unstim.Classical_monocytes_MAPKAPK2       Unstim.Classical_monocytes_MAPKAPK2
## Unstim.Classical_monocytes_IkB                 Unstim.Classical_monocytes_IkB
## Unstim.Classical_monocytes_NFkB               Unstim.Classical_monocytes_NFkB
## Unstim.Classical_monocytes_ERK                 Unstim.Classical_monocytes_ERK
## Unstim.Nonclassical_monocytes_CREB         Unstim.Nonclassical_monocytes_CREB
## Unstim.Nonclassical_monocytes_STAT5       Unstim.Nonclassical_monocytes_STAT5
## Unstim.Nonclassical_monocytes_p38           Unstim.Nonclassical_monocytes_p38
## Unstim.Nonclassical_monocytes_STAT1       Unstim.Nonclassical_monocytes_STAT1
## Unstim.Nonclassical_monocytes_STAT3       Unstim.Nonclassical_monocytes_STAT3
## Unstim.Nonclassical_monocytes_S6             Unstim.Nonclassical_monocytes_S6
## Unstim.Nonclassical_monocytes_MAPKAPK2 Unstim.Nonclassical_monocytes_MAPKAPK2
## Unstim.Nonclassical_monocytes_IkB           Unstim.Nonclassical_monocytes_IkB
## Unstim.Nonclassical_monocytes_NFkB         Unstim.Nonclassical_monocytes_NFkB
## Unstim.Nonclassical_monocytes_ERK           Unstim.Nonclassical_monocytes_ERK
## Unstim.cDCs_CREB                                             Unstim.cDCs_CREB
## Unstim.cDCs_STAT5                                           Unstim.cDCs_STAT5
## Unstim.cDCs_p38                                               Unstim.cDCs_p38
## Unstim.cDCs_STAT1                                           Unstim.cDCs_STAT1
## Unstim.cDCs_STAT3                                           Unstim.cDCs_STAT3
## Unstim.cDCs_S6                                                 Unstim.cDCs_S6
## Unstim.cDCs_MAPKAPK2                                     Unstim.cDCs_MAPKAPK2
## Unstim.cDCs_IkB                                               Unstim.cDCs_IkB
## Unstim.cDCs_NFkB                                             Unstim.cDCs_NFkB
## Unstim.cDCs_ERK                                               Unstim.cDCs_ERK
## Unstim.pDCs_CREB                                             Unstim.pDCs_CREB
## Unstim.pDCs_STAT5                                           Unstim.pDCs_STAT5
## Unstim.pDCs_p38                                               Unstim.pDCs_p38
## Unstim.pDCs_STAT1                                           Unstim.pDCs_STAT1
## Unstim.pDCs_STAT3                                           Unstim.pDCs_STAT3
## Unstim.pDCs_S6                                                 Unstim.pDCs_S6
## Unstim.pDCs_MAPKAPK2                                     Unstim.pDCs_MAPKAPK2
## Unstim.pDCs_IkB                                               Unstim.pDCs_IkB
## Unstim.pDCs_NFkB                                             Unstim.pDCs_NFkB
## Unstim.pDCs_ERK                                               Unstim.pDCs_ERK
## Unstim.Th1_T_cells_CREB                               Unstim.Th1_T_cells_CREB
## Unstim.Th1_T_cells_STAT5                             Unstim.Th1_T_cells_STAT5
## Unstim.Th1_T_cells_p38                                 Unstim.Th1_T_cells_p38
## Unstim.Th1_T_cells_STAT1                             Unstim.Th1_T_cells_STAT1
## Unstim.Th1_T_cells_STAT3                             Unstim.Th1_T_cells_STAT3
## Unstim.Th1_T_cells_S6                                   Unstim.Th1_T_cells_S6
## Unstim.Th1_T_cells_MAPKAPK2                       Unstim.Th1_T_cells_MAPKAPK2
## Unstim.Th1_T_cells_IkB                                 Unstim.Th1_T_cells_IkB
## Unstim.Th1_T_cells_NFkB                               Unstim.Th1_T_cells_NFkB
## Unstim.Th1_T_cells_ERK                                 Unstim.Th1_T_cells_ERK
## Unstim.Intermediate_monocytes_CREB         Unstim.Intermediate_monocytes_CREB
## Unstim.Intermediate_monocytes_STAT5       Unstim.Intermediate_monocytes_STAT5
## Unstim.Intermediate_monocytes_p38           Unstim.Intermediate_monocytes_p38
## Unstim.Intermediate_monocytes_STAT1       Unstim.Intermediate_monocytes_STAT1
## Unstim.Intermediate_monocytes_STAT3       Unstim.Intermediate_monocytes_STAT3
## Unstim.Intermediate_monocytes_S6             Unstim.Intermediate_monocytes_S6
## Unstim.Intermediate_monocytes_MAPKAPK2 Unstim.Intermediate_monocytes_MAPKAPK2
## Unstim.Intermediate_monocytes_IkB           Unstim.Intermediate_monocytes_IkB
## Unstim.Intermediate_monocytes_NFkB         Unstim.Intermediate_monocytes_NFkB
## Unstim.Intermediate_monocytes_ERK           Unstim.Intermediate_monocytes_ERK
## Unstim.MDSCs_CREB                                           Unstim.MDSCs_CREB
## Unstim.MDSCs_STAT5                                         Unstim.MDSCs_STAT5
## Unstim.MDSCs_p38                                             Unstim.MDSCs_p38
## Unstim.MDSCs_STAT1                                         Unstim.MDSCs_STAT1
## Unstim.MDSCs_STAT3                                         Unstim.MDSCs_STAT3
## Unstim.MDSCs_S6                                               Unstim.MDSCs_S6
## Unstim.MDSCs_MAPKAPK2                                   Unstim.MDSCs_MAPKAPK2
## Unstim.MDSCs_IkB                                             Unstim.MDSCs_IkB
## Unstim.MDSCs_NFkB                                           Unstim.MDSCs_NFkB
## Unstim.MDSCs_ERK                                             Unstim.MDSCs_ERK
## Unstim.Tregs_CREB                                           Unstim.Tregs_CREB
## Unstim.Tregs_STAT5                                         Unstim.Tregs_STAT5
## Unstim.Tregs_p38                                             Unstim.Tregs_p38
## Unstim.Tregs_STAT1                                         Unstim.Tregs_STAT1
## Unstim.Tregs_STAT3                                         Unstim.Tregs_STAT3
## Unstim.Tregs_S6                                               Unstim.Tregs_S6
## Unstim.Tregs_MAPKAPK2                                   Unstim.Tregs_MAPKAPK2
## Unstim.Tregs_IkB                                             Unstim.Tregs_IkB
## Unstim.Tregs_NFkB                                           Unstim.Tregs_NFkB
## Unstim.Tregs_ERK                                             Unstim.Tregs_ERK
## Unstim.CD56lo_NK_cells_CREB                       Unstim.CD56lo_NK_cells_CREB
## Unstim.CD56lo_NK_cells_STAT5                     Unstim.CD56lo_NK_cells_STAT5
## Unstim.CD56lo_NK_cells_p38                         Unstim.CD56lo_NK_cells_p38
## Unstim.CD56lo_NK_cells_STAT1                     Unstim.CD56lo_NK_cells_STAT1
## Unstim.CD56lo_NK_cells_STAT3                     Unstim.CD56lo_NK_cells_STAT3
## Unstim.CD56lo_NK_cells_S6                           Unstim.CD56lo_NK_cells_S6
## Unstim.CD56lo_NK_cells_MAPKAPK2               Unstim.CD56lo_NK_cells_MAPKAPK2
## Unstim.CD56lo_NK_cells_IkB                         Unstim.CD56lo_NK_cells_IkB
## Unstim.CD56lo_NK_cells_NFkB                       Unstim.CD56lo_NK_cells_NFkB
## Unstim.CD56lo_NK_cells_ERK                         Unstim.CD56lo_NK_cells_ERK
## Unstim.CD56hi_NK_cells_CREB                       Unstim.CD56hi_NK_cells_CREB
## Unstim.CD56hi_NK_cells_STAT5                     Unstim.CD56hi_NK_cells_STAT5
## Unstim.CD56hi_NK_cells_p38                         Unstim.CD56hi_NK_cells_p38
## Unstim.CD56hi_NK_cells_STAT1                     Unstim.CD56hi_NK_cells_STAT1
## Unstim.CD56hi_NK_cells_STAT3                     Unstim.CD56hi_NK_cells_STAT3
## Unstim.CD56hi_NK_cells_S6                           Unstim.CD56hi_NK_cells_S6
## Unstim.CD56hi_NK_cells_MAPKAPK2               Unstim.CD56hi_NK_cells_MAPKAPK2
## Unstim.CD56hi_NK_cells_IkB                         Unstim.CD56hi_NK_cells_IkB
## Unstim.CD56hi_NK_cells_NFkB                       Unstim.CD56hi_NK_cells_NFkB
## Unstim.CD56hi_NK_cells_ERK                         Unstim.CD56hi_NK_cells_ERK
## Unstim.gd_T_cells_CREB                                 Unstim.gd_T_cells_CREB
## Unstim.gd_T_cells_STAT5                               Unstim.gd_T_cells_STAT5
## Unstim.gd_T_cells_p38                                   Unstim.gd_T_cells_p38
## Unstim.gd_T_cells_STAT1                               Unstim.gd_T_cells_STAT1
## Unstim.gd_T_cells_STAT3                               Unstim.gd_T_cells_STAT3
## Unstim.gd_T_cells_S6                                     Unstim.gd_T_cells_S6
## Unstim.gd_T_cells_MAPKAPK2                         Unstim.gd_T_cells_MAPKAPK2
## Unstim.gd_T_cells_IkB                                   Unstim.gd_T_cells_IkB
## Unstim.gd_T_cells_NFkB                                 Unstim.gd_T_cells_NFkB
## Unstim.gd_T_cells_ERK                                   Unstim.gd_T_cells_ERK
## Unstim.Memory_CD4_T_cells_CREB                 Unstim.Memory_CD4_T_cells_CREB
## Unstim.Memory_CD4_T_cells_STAT5               Unstim.Memory_CD4_T_cells_STAT5
## Unstim.Memory_CD4_T_cells_p38                   Unstim.Memory_CD4_T_cells_p38
## Unstim.Memory_CD4_T_cells_STAT1               Unstim.Memory_CD4_T_cells_STAT1
## Unstim.Memory_CD4_T_cells_STAT3               Unstim.Memory_CD4_T_cells_STAT3
## Unstim.Memory_CD4_T_cells_S6                     Unstim.Memory_CD4_T_cells_S6
## Unstim.Memory_CD4_T_cells_MAPKAPK2         Unstim.Memory_CD4_T_cells_MAPKAPK2
## Unstim.Memory_CD4_T_cells_IkB                   Unstim.Memory_CD4_T_cells_IkB
## Unstim.Memory_CD4_T_cells_NFkB                 Unstim.Memory_CD4_T_cells_NFkB
## Unstim.Memory_CD4_T_cells_ERK                   Unstim.Memory_CD4_T_cells_ERK

Here’s for LPS and Cocktail only:

plot_p_v_up(dfs = list("LPS" = LPS_df, "Cocktail" = Cocktail_df), sampleType = sampleType,  paired_output = list("LPS" = paired_output$LPS, "Cocktail" = paired_output$Cocktail), unpaired_output = list("LPS" = unpaired_output$LPS, "Cocktail" = unpaired_output$Cocktail))

##  [1] "LPS.Granulocytes_MAPKAPK2"               
##  [2] "LPS.Intermediate_monocytes_CREB"         
##  [3] "LPS.Granulocytes_NFkB"                   
##  [4] "LPS.cDCs_ERK"                            
##  [5] "LPS.Granulocytes_p38"                    
##  [6] "LPS.Nonclassical_monocytes_S6"           
##  [7] "LPS.Th1_T_cells_IkB"                     
##  [8] "LPS.Classical_monocytes_ERK"             
##  [9] "LPS.Intermediate_monocytes_S6"           
## [10] "LPS.Memory_CD8_T_cells_S6"               
## [11] "LPS.Granulocytes_STAT1"                  
## [12] "LPS.Intermediate_monocytes_ERK"          
## [13] "LPS.Th1_T_cells_STAT1"                   
## [14] "LPS.Th1_T_cells_STAT5"                   
## [15] "LPS.Nonclassical_monocytes_CREB"         
## [16] "LPS.cDCs_MAPKAPK2"                       
## [17] "LPS.Th1_T_cells_STAT3"                   
## [18] "LPS.Th1_T_cells_CREB"                    
## [19] "LPS.Classical_monocytes_MAPKAPK2"        
## [20] "LPS.CD56lo_NK_cells_CREB"                
## [21] "LPS.Memory_CD8_T_cells_CREB"             
## [22] "LPS.B_cells_ERK"                         
## [23] "LPS.Th1_T_cells_ERK"                     
## [24] "LPS.pDCs_S6"                             
## [25] "LPS.pDCs_ERK"                            
## [26] "LPS.Memory_CD4_T_cells_p38"              
## [27] "LPS.Tregs_STAT1"                         
## [28] "LPS.Th1_T_cells_p38"                     
## [29] "LPS.CD56hi_NK_cells_CREB"                
## [30] "LPS.Granulocytes_CREB"                   
## [31] "LPS.Tregs_CREB"                          
## [32] "LPS.Th1_T_cells_S6"                      
## [33] "LPS.CD56hi_NK_cells_ERK"                 
## [34] "LPS.Th1_T_cells_MAPKAPK2"                
## [35] "LPS.pDCs_STAT3"                          
## [36] "LPS.Tregs_ERK"                           
## [37] "LPS.Tregs_p38"                           
## [38] "LPS.cDCs_p38"                            
## [39] "LPS.B_cells_STAT5"                       
## [40] "LPS.cDCs_CREB"                           
## [41] "LPS.Naive_CD4_T_cells_ERK"               
## [42] "LPS.Intermediate_monocytes_IkB"          
## [43] "Cocktail.Classical_monocytes_STAT1"      
## [44] "Cocktail.cDCs_STAT1"                     
## [45] "Cocktail.Tregs_STAT1"                    
## [46] "Cocktail.CD56lo_NK_cells_STAT1"          
## [47] "Cocktail.Naive_CD4_T_cells_STAT1"        
## [48] "Cocktail.CD4_T_cells_STAT1"              
## [49] "Cocktail.CD56hi_NK_cells_STAT1"          
## [50] "Cocktail.Classical_monocytes_STAT3"      
## [51] "Cocktail.cDCs_STAT3"                     
## [52] "Cocktail.Intermediate_monocytes_STAT1"   
## [53] "Cocktail.pDCs_STAT5"                     
## [54] "Cocktail.Memory_CD4_T_cells_STAT1"       
## [55] "Cocktail.gd_T_cells_STAT1"               
## [56] "Cocktail.MDSCs_STAT3"                    
## [57] "Cocktail.Intermediate_monocytes_CREB"    
## [58] "Cocktail.pDCs_STAT1"                     
## [59] "Cocktail.Granulocytes_STAT1"             
## [60] "Cocktail.pDCs_STAT3"                     
## [61] "Cocktail.Nonclassical_monocytes_STAT1"   
## [62] "Cocktail.Nonclassical_monocytes_S6"      
## [63] "Cocktail.Naive_CD8_T_cells_STAT1"        
## [64] "Cocktail.CD56lo_NK_cells_STAT3"          
## [65] "Cocktail.Memory_CD8_T_cells_CREB"        
## [66] "Cocktail.Intermediate_monocytes_STAT3"   
## [67] "Cocktail.Intermediate_monocytes_S6"      
## [68] "Cocktail.MDSCs_STAT1"                    
## [69] "Cocktail.Nonclassical_monocytes_CREB"    
## [70] "Cocktail.B_cells_STAT1"                  
## [71] "Cocktail.CD56lo_NK_cells_S6"             
## [72] "Cocktail.Memory_CD8_T_cells_S6"          
## [73] "Cocktail.Th1_T_cells_ERK"                
## [74] "Cocktail.pDCs_ERK"                       
## [75] "Cocktail.CD56lo_NK_cells_CREB"           
## [76] "Cocktail.Granulocytes_NFkB"              
## [77] "Cocktail.CD56lo_NK_cells_ERK"            
## [78] "Cocktail.Granulocytes_p38"               
## [79] "Cocktail.Naive_CD8_T_cells_STAT5"        
## [80] "Cocktail.Naive_CD4_T_cells_STAT5"        
## [81] "Cocktail.Memory_CD8_T_cells_STAT3"       
## [82] "Cocktail.CD8_T_cells_STAT5"              
## [83] "Cocktail.CD8_T_cells_STAT3"              
## [84] "Cocktail.CD4_T_cells_STAT5"              
## [85] "Cocktail.gd_T_cells_STAT5"               
## [86] "Cocktail.Memory_CD4_T_cells_STAT5"       
## [87] "Cocktail.Intermediate_monocytes_MAPKAPK2"
## [88] "Cocktail.CD56hi_NK_cells_MAPKAPK2"       
## [89] "Cocktail.gd_T_cells_STAT3"               
##  [1] "LPS.cDCs_ERK"                            
##  [2] "LPS.Intermediate_monocytes_CREB"         
##  [3] "LPS.Classical_monocytes_ERK"             
##  [4] "LPS.Granulocytes_MAPKAPK2"               
##  [5] "LPS.Th1_T_cells_IkB"                     
##  [6] "LPS.Granulocytes_NFkB"                   
##  [7] "LPS.cDCs_MAPKAPK2"                       
##  [8] "LPS.Th1_T_cells_STAT1"                   
##  [9] "LPS.Th1_T_cells_STAT5"                   
## [10] "LPS.Classical_monocytes_MAPKAPK2"        
## [11] "LPS.Nonclassical_monocytes_S6"           
## [12] "LPS.Intermediate_monocytes_ERK"          
## [13] "LPS.Th1_T_cells_ERK"                     
## [14] "LPS.B_cells_ERK"                         
## [15] "LPS.Granulocytes_p38"                    
## [16] "LPS.CD56lo_NK_cells_CREB"                
## [17] "LPS.Granulocytes_STAT1"                  
## [18] "LPS.Intermediate_monocytes_S6"           
## [19] "LPS.Th1_T_cells_STAT3"                   
## [20] "LPS.Th1_T_cells_CREB"                    
## [21] "LPS.Memory_CD8_T_cells_S6"               
## [22] "LPS.Tregs_STAT1"                         
## [23] "LPS.pDCs_S6"                             
## [24] "LPS.Th1_T_cells_p38"                     
## [25] "LPS.Memory_CD4_T_cells_p38"              
## [26] "LPS.Memory_CD8_T_cells_CREB"             
## [27] "LPS.Tregs_CREB"                          
## [28] "LPS.Tregs_p38"                           
## [29] "LPS.pDCs_STAT3"                          
## [30] "LPS.Th1_T_cells_MAPKAPK2"                
## [31] "LPS.Th1_T_cells_S6"                      
## [32] "LPS.B_cells_STAT5"                       
## [33] "LPS.CD56hi_NK_cells_ERK"                 
## [34] "LPS.Tregs_ERK"                           
## [35] "LPS.Intermediate_monocytes_STAT3"        
## [36] "LPS.pDCs_ERK"                            
## [37] "LPS.CD56hi_NK_cells_CREB"                
## [38] "LPS.Naive_CD4_T_cells_ERK"               
## [39] "LPS.Memory_CD8_T_cells_p38"              
## [40] "LPS.Nonclassical_monocytes_CREB"         
## [41] "LPS.pDCs_CREB"                           
## [42] "LPS.Granulocytes_CREB"                   
## [43] "LPS.Naive_CD4_T_cells_IkB"               
## [44] "LPS.cDCs_S6"                             
## [45] "LPS.Naive_CD8_T_cells_IkB"               
## [46] "LPS.Memory_CD4_T_cells_STAT1"            
## [47] "LPS.cDCs_CREB"                           
## [48] "LPS.gd_T_cells_S6"                       
## [49] "LPS.CD56lo_NK_cells_STAT1"               
## [50] "LPS.B_cells_S6"                          
## [51] "Cocktail.Classical_monocytes_STAT1"      
## [52] "Cocktail.cDCs_STAT1"                     
## [53] "Cocktail.CD56lo_NK_cells_STAT1"          
## [54] "Cocktail.CD56hi_NK_cells_STAT1"          
## [55] "Cocktail.Naive_CD4_T_cells_STAT1"        
## [56] "Cocktail.Classical_monocytes_STAT3"      
## [57] "Cocktail.Intermediate_monocytes_STAT1"   
## [58] "Cocktail.Tregs_STAT1"                    
## [59] "Cocktail.cDCs_STAT3"                     
## [60] "Cocktail.CD4_T_cells_STAT1"              
## [61] "Cocktail.Memory_CD8_T_cells_CREB"        
## [62] "Cocktail.pDCs_STAT1"                     
## [63] "Cocktail.pDCs_STAT5"                     
## [64] "Cocktail.Intermediate_monocytes_CREB"    
## [65] "Cocktail.Intermediate_monocytes_STAT3"   
## [66] "Cocktail.MDSCs_STAT3"                    
## [67] "Cocktail.Memory_CD4_T_cells_STAT1"       
## [68] "Cocktail.gd_T_cells_STAT1"               
## [69] "Cocktail.pDCs_STAT3"                     
## [70] "Cocktail.Nonclassical_monocytes_CREB"    
## [71] "Cocktail.MDSCs_STAT1"                    
## [72] "Cocktail.Granulocytes_STAT1"             
## [73] "Cocktail.Naive_CD8_T_cells_STAT1"        
## [74] "Cocktail.Nonclassical_monocytes_S6"      
## [75] "Cocktail.CD56lo_NK_cells_STAT3"          
## [76] "Cocktail.Memory_CD8_T_cells_S6"          
## [77] "Cocktail.Th1_T_cells_ERK"                
## [78] "Cocktail.Intermediate_monocytes_S6"      
## [79] "Cocktail.CD56lo_NK_cells_CREB"           
## [80] "Cocktail.Granulocytes_NFkB"              
## [81] "Cocktail.pDCs_ERK"                       
## [82] "Cocktail.gd_T_cells_CREB"                
## [83] "Cocktail.B_cells_STAT1"                  
## [84] "Cocktail.Naive_CD4_T_cells_STAT5"        
## [85] "Cocktail.Naive_CD8_T_cells_STAT5"        
## [86] "Cocktail.CD8_T_cells_STAT5"              
## [87] "Cocktail.CD4_T_cells_STAT5"              
## [88] "Cocktail.Memory_CD8_T_cells_STAT3"       
## [89] "Cocktail.Memory_CD4_T_cells_STAT5"       
## [90] "Cocktail.gd_T_cells_STAT5"               
## [91] "Cocktail.CD56hi_NK_cells_MAPKAPK2"       
## [92] "Cocktail.Intermediate_monocytes_MAPKAPK2"
## [93] "Cocktail.CD8_T_cells_STAT3"              
##   [1]  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
##  [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [34] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [45] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [56]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [67] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
##  [78] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE
##  [89] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE
## [100]  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE
## [111]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE
## [122] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
## [144]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE
## [155] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [166] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [177] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [188] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE
## [199]  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [210] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [221] FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [232]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE
## [243] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [254]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [265]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE
## [276]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [287] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE
## [298] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [309] FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE
## [320] FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE
## [331] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [342] FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE
## [353] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE
## [364]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
## [375] FALSE FALSE FALSE FALSE FALSE FALSE
##   [1]  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
##  [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [34] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE
##  [45] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
##  [56]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE
##  [67] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
##  [78] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE
##  [89] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE
## [100]  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE
## [111]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE
## [122] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
## [144]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE
## [155] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [166] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE
## [177] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE
## [188] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [199]  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [210] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [221] FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [232]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE
## [243] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [254]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [265]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE
## [276]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [287] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE
## [298] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [309] FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE
## [320] FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE
## [331] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
## [342] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [353] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE
## [364]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
## [375] FALSE FALSE FALSE FALSE FALSE FALSE

##                                          unpaired_pvals paired_pvals
## LPS.Granulocytes_CREB                      3.783763e-02 2.643708e-02
## LPS.Granulocytes_STAT5                     1.625649e-01 9.762420e-02
## LPS.Granulocytes_p38                       1.949800e-03 6.686237e-04
## LPS.Granulocytes_STAT1                     1.090521e-03 7.387796e-04
## LPS.Granulocytes_STAT3                     6.254134e-02 6.730100e-02
## LPS.Granulocytes_S6                        4.989709e-01 3.994294e-01
## LPS.Granulocytes_MAPKAPK2                  1.802462e-04 1.857843e-04
## LPS.Granulocytes_IkB                       2.455289e-01 1.540945e-01
## LPS.Granulocytes_NFkB                      4.832534e-05 1.262582e-04
## LPS.Granulocytes_ERK                       1.906192e-01 1.422160e-01
## LPS.CD8_T_cells_CREB                       8.995880e-02 4.850847e-02
## LPS.CD8_T_cells_STAT5                      1.121871e-01 1.658291e-01
## LPS.CD8_T_cells_p38                        5.523849e-03 1.481440e-02
## LPS.CD8_T_cells_STAT1                      9.345168e-02 1.218269e-01
## LPS.CD8_T_cells_STAT3                      2.363703e-01 3.094741e-01
## LPS.CD8_T_cells_S6                         4.218953e-03 1.010782e-02
## LPS.CD8_T_cells_MAPKAPK2                   1.312338e-01 2.100037e-01
## LPS.CD8_T_cells_IkB                        4.404673e-02 9.638713e-02
## LPS.CD8_T_cells_NFkB                       8.720223e-02 1.382374e-01
## LPS.CD8_T_cells_ERK                        4.637117e-02 7.781786e-02
## LPS.CD4_T_cells_CREB                       3.784971e-02 5.177601e-02
## LPS.CD4_T_cells_STAT5                      3.008470e-01 3.841470e-01
## LPS.CD4_T_cells_p38                        1.875365e-03 7.278507e-03
## LPS.CD4_T_cells_STAT1                      3.325704e-03 1.111920e-02
## LPS.CD4_T_cells_STAT3                      7.468565e-01 7.555742e-01
## LPS.CD4_T_cells_S6                         1.563098e-02 4.702247e-02
## LPS.CD4_T_cells_MAPKAPK2                   2.256486e-01 3.192959e-01
## LPS.CD4_T_cells_IkB                        6.039628e-03 2.576573e-02
## LPS.CD4_T_cells_NFkB                       8.750321e-02 1.327405e-01
## LPS.CD4_T_cells_ERK                        2.184896e-02 4.150028e-02
## LPS.Naive_CD4_T_cells_CREB                 1.664633e-01 2.022860e-01
## LPS.Naive_CD4_T_cells_STAT5                8.856334e-02 1.313583e-01
## LPS.Naive_CD4_T_cells_p38                  1.750436e-02 5.074675e-02
## LPS.Naive_CD4_T_cells_STAT1                3.706196e-03 8.058377e-03
## LPS.Naive_CD4_T_cells_STAT3                2.720142e-01 3.041328e-01
## LPS.Naive_CD4_T_cells_S6                   3.817540e-02 9.200947e-02
## LPS.Naive_CD4_T_cells_MAPKAPK2             3.811198e-01 4.829166e-01
## LPS.Naive_CD4_T_cells_IkB                  2.263725e-03 1.369260e-02
## LPS.Naive_CD4_T_cells_NFkB                 2.432129e-01 3.262682e-01
## LPS.Naive_CD4_T_cells_ERK                  5.947531e-03 1.250720e-02
## LPS.Naive_CD8_T_cells_CREB                 6.085781e-01 6.159240e-01
## LPS.Naive_CD8_T_cells_STAT5                2.006932e-02 4.825051e-02
## LPS.Naive_CD8_T_cells_p38                  2.552659e-02 5.201532e-02
## LPS.Naive_CD8_T_cells_STAT1                4.533740e-02 6.180609e-02
## LPS.Naive_CD8_T_cells_STAT3                4.434606e-02 9.929234e-02
## LPS.Naive_CD8_T_cells_S6                   8.434542e-02 1.865535e-01
## LPS.Naive_CD8_T_cells_MAPKAPK2             2.819456e-01 4.052953e-01
## LPS.Naive_CD8_T_cells_IkB                  3.193868e-03 1.374692e-02
## LPS.Naive_CD8_T_cells_NFkB                 1.912033e-01 2.662679e-01
## LPS.Naive_CD8_T_cells_ERK                  1.923678e-02 4.268931e-02
## LPS.Memory_CD8_T_cells_CREB                1.002414e-03 3.572267e-04
## LPS.Memory_CD8_T_cells_STAT5               1.496193e-01 1.598064e-01
## LPS.Memory_CD8_T_cells_p38                 8.087042e-04 5.756421e-03
## LPS.Memory_CD8_T_cells_STAT1               4.768323e-02 9.429568e-02
## LPS.Memory_CD8_T_cells_STAT3               4.125815e-01 5.023914e-01
## LPS.Memory_CD8_T_cells_S6                  1.427250e-04 2.013783e-05
## LPS.Memory_CD8_T_cells_MAPKAPK2            1.394502e-01 1.703192e-01
## LPS.Memory_CD8_T_cells_IkB                 9.722163e-02 1.916266e-01
## LPS.Memory_CD8_T_cells_NFkB                1.158359e-01 1.678764e-01
## LPS.Memory_CD8_T_cells_ERK                 9.189339e-02 1.137438e-01
## LPS.B_cells_CREB                           1.688791e-01 1.340869e-01
## LPS.B_cells_STAT5                          2.638342e-04 3.810488e-03
## LPS.B_cells_p38                            1.784604e-01 1.577801e-01
## LPS.B_cells_STAT1                          2.210770e-02 2.818577e-02
## LPS.B_cells_STAT3                          1.145218e-03 3.969543e-03
## LPS.B_cells_S6                             1.018298e-02 1.854926e-02
## LPS.B_cells_MAPKAPK2                       9.023285e-01 9.188352e-01
## LPS.B_cells_IkB                            7.304628e-01 7.153502e-01
## LPS.B_cells_NFkB                           9.405601e-01 9.362869e-01
## LPS.B_cells_ERK                            3.164204e-04 2.349311e-03
## LPS.Classical_monocytes_CREB               7.697039e-02 7.355686e-02
## LPS.Classical_monocytes_STAT5              4.168298e-01 4.604080e-01
## LPS.Classical_monocytes_p38                6.567651e-02 5.213851e-02
## LPS.Classical_monocytes_STAT1              3.393272e-01 3.237891e-01
## LPS.Classical_monocytes_STAT3              3.633153e-01 3.528241e-01
## LPS.Classical_monocytes_S6                 5.295564e-02 6.889808e-02
## LPS.Classical_monocytes_MAPKAPK2           3.442018e-04 4.257396e-03
## LPS.Classical_monocytes_IkB                5.301733e-01 4.299975e-01
## LPS.Classical_monocytes_NFkB               8.241754e-02 5.096554e-02
## LPS.Classical_monocytes_ERK                2.980821e-05 5.865644e-04
## LPS.Nonclassical_monocytes_CREB            3.721711e-02 4.308902e-03
## LPS.Nonclassical_monocytes_STAT5           9.098006e-01 9.061150e-01
## LPS.Nonclassical_monocytes_p38             3.985547e-01 1.140778e-01
## LPS.Nonclassical_monocytes_STAT1           5.819131e-01 4.504055e-01
## LPS.Nonclassical_monocytes_STAT3           2.098742e-01 2.241985e-01
## LPS.Nonclassical_monocytes_S6              1.508872e-03 8.007305e-04
## LPS.Nonclassical_monocytes_MAPKAPK2        9.518378e-01 9.392337e-01
## LPS.Nonclassical_monocytes_IkB             2.018135e-01 4.718950e-03
## LPS.Nonclassical_monocytes_NFkB            5.591591e-01 5.041067e-01
## LPS.Nonclassical_monocytes_ERK             5.248101e-01 4.548691e-01
## LPS.cDCs_CREB                              4.463392e-02 4.330073e-02
## LPS.cDCs_STAT5                             3.475004e-01 3.752976e-01
## LPS.cDCs_p38                               5.102548e-02 4.372824e-02
## LPS.cDCs_STAT1                             3.750960e-01 3.765760e-01
## LPS.cDCs_STAT3                             2.200325e-01 1.894526e-01
## LPS.cDCs_S6                                4.111547e-02 5.462969e-02
## LPS.cDCs_MAPKAPK2                          1.520158e-04 3.370337e-03
## LPS.cDCs_IkB                               8.088105e-01 7.414717e-01
## LPS.cDCs_NFkB                              8.281548e-02 4.839562e-02
## LPS.cDCs_ERK                               6.900363e-06 2.456489e-04
## LPS.pDCs_CREB                              4.790057e-02 7.502808e-02
## LPS.pDCs_STAT5                             2.195491e-01 7.898268e-02
## LPS.pDCs_p38                               1.192723e-01 1.264610e-01
## LPS.pDCs_STAT1                             8.424139e-02 6.498668e-02
## LPS.pDCs_STAT3                             7.655393e-03 2.013856e-02
## LPS.pDCs_S6                                1.287328e-02 8.605304e-03
## LPS.pDCs_MAPKAPK2                          1.628653e-01 1.295491e-01
## LPS.pDCs_IkB                               4.295403e-01 4.827252e-01
## LPS.pDCs_NFkB                              5.443848e-01 5.302885e-01
## LPS.pDCs_ERK                               3.259542e-02 1.167659e-02
## LPS.Th1_T_cells_CREB                       1.072605e-03 1.180558e-03
## LPS.Th1_T_cells_STAT5                      1.627107e-04 1.250588e-03
## LPS.Th1_T_cells_p38                        5.247840e-04 4.526139e-03
## LPS.Th1_T_cells_STAT1                      1.522706e-04 3.481618e-04
## LPS.Th1_T_cells_STAT3                      3.383236e-04 4.152809e-04
## LPS.Th1_T_cells_S6                         1.057288e-02 2.022629e-02
## LPS.Th1_T_cells_MAPKAPK2                   4.409969e-03 1.289875e-02
## LPS.Th1_T_cells_IkB                        1.552394e-04 2.727190e-04
## LPS.Th1_T_cells_NFkB                       1.294246e-01 2.038822e-01
## LPS.Th1_T_cells_ERK                        5.697479e-04 4.099494e-03
## LPS.Intermediate_monocytes_CREB            2.486140e-04 4.002258e-04
## LPS.Intermediate_monocytes_STAT5           3.005911e-01 2.657163e-01
## LPS.Intermediate_monocytes_p38             6.780650e-01 5.091597e-01
## LPS.Intermediate_monocytes_STAT1           4.634725e-03 5.016941e-03
## LPS.Intermediate_monocytes_STAT3           1.222113e-02 2.953397e-02
## LPS.Intermediate_monocytes_S6              2.524553e-03 1.032253e-03
## LPS.Intermediate_monocytes_MAPKAPK2        4.596377e-01 4.907907e-01
## LPS.Intermediate_monocytes_IkB             8.448468e-02 3.552542e-02
## LPS.Intermediate_monocytes_NFkB            5.854665e-02 4.172859e-02
## LPS.Intermediate_monocytes_ERK             8.155799e-04 1.414061e-03
## LPS.MDSCs_CREB                             4.439090e-01 3.859424e-01
## LPS.MDSCs_STAT5                            7.505726e-01 7.589233e-01
## LPS.MDSCs_p38                              5.064226e-01 4.147920e-01
## LPS.MDSCs_STAT1                            8.179251e-01 7.919136e-01
## LPS.MDSCs_STAT3                            1.021537e-01 2.109153e-01
## LPS.MDSCs_S6                               3.776016e-01 3.686788e-01
## LPS.MDSCs_MAPKAPK2                         8.929331e-01 8.789827e-01
## LPS.MDSCs_IkB                              4.683011e-01 3.429283e-01
## LPS.MDSCs_NFkB                             6.688987e-01 5.848676e-01
## LPS.MDSCs_ERK                              6.659650e-01 5.945577e-01
## LPS.Tregs_CREB                             1.111851e-03 7.053751e-03
## LPS.Tregs_STAT5                            6.884383e-02 9.076124e-03
## LPS.Tregs_p38                              2.245698e-03 1.090497e-02
## LPS.Tregs_STAT1                            4.891992e-04 3.608167e-03
## LPS.Tregs_STAT3                            9.408616e-01 9.443341e-01
## LPS.Tregs_S6                               1.750596e-01 2.536198e-01
## LPS.Tregs_MAPKAPK2                         4.159939e-01 4.838047e-01
## LPS.Tregs_IkB                              1.723351e-01 2.528793e-01
## LPS.Tregs_NFkB                             4.308424e-01 5.076842e-01
## LPS.Tregs_ERK                              1.152097e-02 1.708144e-02
## LPS.CD56lo_NK_cells_CREB                   5.013129e-05 5.502187e-04
## LPS.CD56lo_NK_cells_STAT5                  5.116511e-01 5.529819e-01
## LPS.CD56lo_NK_cells_p38                    3.415222e-01 4.095811e-01
## LPS.CD56lo_NK_cells_STAT1                  3.112305e-03 2.360121e-02
## LPS.CD56lo_NK_cells_STAT3                  3.063608e-01 4.254197e-01
## LPS.CD56lo_NK_cells_S6                     1.117189e-01 1.482539e-01
## LPS.CD56lo_NK_cells_MAPKAPK2               2.181960e-01 3.319048e-01
## LPS.CD56lo_NK_cells_IkB                    6.356498e-01 6.856536e-01
## LPS.CD56lo_NK_cells_NFkB                   4.049508e-01 4.359202e-01
## LPS.CD56lo_NK_cells_ERK                    1.201455e-01 1.846198e-01
## LPS.CD56hi_NK_cells_CREB                   9.768998e-03 4.914787e-03
## LPS.CD56hi_NK_cells_STAT5                  9.249209e-01 9.084947e-01
## LPS.CD56hi_NK_cells_p38                    3.906871e-01 4.159952e-01
## LPS.CD56hi_NK_cells_STAT1                  3.246819e-01 3.197096e-01
## LPS.CD56hi_NK_cells_STAT3                  3.646850e-01 3.103363e-01
## LPS.CD56hi_NK_cells_S6                     3.229003e-02 1.262770e-02
## LPS.CD56hi_NK_cells_MAPKAPK2               1.949345e-02 3.306435e-03
## LPS.CD56hi_NK_cells_IkB                    6.552864e-01 6.317264e-01
## LPS.CD56hi_NK_cells_NFkB                   2.391147e-01 2.489655e-01
## LPS.CD56hi_NK_cells_ERK                    6.713890e-03 1.308747e-02
## LPS.gd_T_cells_CREB                        6.889516e-02 5.211790e-02
## LPS.gd_T_cells_STAT5                       5.747189e-01 6.137692e-01
## LPS.gd_T_cells_p38                         9.157938e-03 2.894868e-02
## LPS.gd_T_cells_STAT1                       2.170140e-02 2.874559e-02
## LPS.gd_T_cells_STAT3                       3.906916e-01 2.886266e-01
## LPS.gd_T_cells_S6                          1.610006e-02 2.294261e-02
## LPS.gd_T_cells_MAPKAPK2                    1.703086e-01 2.400310e-01
## LPS.gd_T_cells_IkB                         2.180042e-01 2.794451e-01
## LPS.gd_T_cells_NFkB                        2.407166e-01 2.820138e-01
## LPS.gd_T_cells_ERK                         7.423228e-02 1.583610e-01
## LPS.Memory_CD4_T_cells_CREB                5.949051e-03 7.466765e-03
## LPS.Memory_CD4_T_cells_STAT5               6.114509e-01 6.636549e-01
## LPS.Memory_CD4_T_cells_p38                 1.696984e-04 9.710320e-04
## LPS.Memory_CD4_T_cells_STAT1               1.587635e-03 9.920857e-03
## LPS.Memory_CD4_T_cells_STAT3               7.188818e-01 7.397369e-01
## LPS.Memory_CD4_T_cells_S6                  5.404505e-02 8.560727e-02
## LPS.Memory_CD4_T_cells_MAPKAPK2            1.361428e-01 2.102232e-01
## LPS.Memory_CD4_T_cells_IkB                 3.582133e-02 6.368846e-02
## LPS.Memory_CD4_T_cells_NFkB                8.118870e-02 1.096778e-01
## LPS.Memory_CD4_T_cells_ERK                 2.943559e-02 5.272070e-02
## Cocktail.Granulocytes_CREB                 1.372723e-01 7.654011e-02
## Cocktail.Granulocytes_STAT5                6.036978e-02 7.086786e-02
## Cocktail.Granulocytes_p38                  3.969318e-02 1.087332e-02
## Cocktail.Granulocytes_STAT1                3.729284e-03 1.390396e-03
## Cocktail.Granulocytes_STAT3                7.332063e-01 7.430882e-01
## Cocktail.Granulocytes_S6                   8.244039e-01 7.600163e-01
## Cocktail.Granulocytes_MAPKAPK2             6.410404e-01 6.039015e-01
## Cocktail.Granulocytes_IkB                  2.413524e-01 3.098739e-01
## Cocktail.Granulocytes_NFkB                 8.494146e-03 1.298083e-02
## Cocktail.Granulocytes_ERK                  1.591356e-01 9.849303e-02
## Cocktail.CD8_T_cells_CREB                  1.105485e-02 4.894132e-02
## Cocktail.CD8_T_cells_STAT5                 7.405472e-05 1.382645e-04
## Cocktail.CD8_T_cells_p38                   2.610063e-01 8.181273e-02
## Cocktail.CD8_T_cells_STAT1                 1.957775e-01 1.296004e-01
## Cocktail.CD8_T_cells_STAT3                 4.144848e-03 2.078093e-04
## Cocktail.CD8_T_cells_S6                    2.583585e-03 7.600890e-03
## Cocktail.CD8_T_cells_MAPKAPK2              1.324119e-01 2.030600e-01
## Cocktail.CD8_T_cells_IkB                   7.935428e-01 7.705339e-01
## Cocktail.CD8_T_cells_NFkB                  3.213584e-01 2.971104e-01
## Cocktail.CD8_T_cells_ERK                   7.487132e-02 7.435372e-02
## Cocktail.CD4_T_cells_CREB                  7.619189e-01 8.016618e-01
## Cocktail.CD4_T_cells_STAT5                 6.778096e-05 6.181327e-04
## Cocktail.CD4_T_cells_p38                   9.860246e-01 9.573985e-01
## Cocktail.CD4_T_cells_STAT1                 3.912789e-05 1.411548e-05
## Cocktail.CD4_T_cells_STAT3                 2.856236e-01 2.282371e-01
## Cocktail.CD4_T_cells_S6                    2.146608e-03 1.736947e-03
## Cocktail.CD4_T_cells_MAPKAPK2              1.190015e-02 3.450640e-02
## Cocktail.CD4_T_cells_IkB                   7.981989e-01 7.797428e-01
## Cocktail.CD4_T_cells_NFkB                  2.197953e-02 1.854070e-02
## Cocktail.CD4_T_cells_ERK                   6.194067e-01 6.048827e-01
## Cocktail.Naive_CD4_T_cells_CREB            3.560716e-01 3.747882e-01
## Cocktail.Naive_CD4_T_cells_STAT5           9.217475e-07 3.690274e-05
## Cocktail.Naive_CD4_T_cells_p38             3.550968e-01 1.144599e-02
## Cocktail.Naive_CD4_T_cells_STAT1           1.387196e-05 1.055501e-05
## Cocktail.Naive_CD4_T_cells_STAT3           3.611570e-01 2.923945e-01
## Cocktail.Naive_CD4_T_cells_S6              3.018856e-02 1.979025e-02
## Cocktail.Naive_CD4_T_cells_MAPKAPK2        1.685303e-02 4.886949e-02
## Cocktail.Naive_CD4_T_cells_IkB             5.198827e-01 5.086278e-01
## Cocktail.Naive_CD4_T_cells_NFkB            9.153930e-03 1.503021e-02
## Cocktail.Naive_CD4_T_cells_ERK             5.523448e-01 5.549189e-01
## Cocktail.Naive_CD8_T_cells_CREB            6.827006e-01 7.561352e-01
## Cocktail.Naive_CD8_T_cells_STAT5           1.506443e-06 1.590328e-05
## Cocktail.Naive_CD8_T_cells_p38             2.454057e-01 3.577070e-02
## Cocktail.Naive_CD8_T_cells_STAT1           4.841112e-03 2.232547e-03
## Cocktail.Naive_CD8_T_cells_STAT3           1.353675e-01 1.016751e-02
## Cocktail.Naive_CD8_T_cells_S6              5.829137e-02 5.949012e-02
## Cocktail.Naive_CD8_T_cells_MAPKAPK2        5.192037e-02 1.118558e-01
## Cocktail.Naive_CD8_T_cells_IkB             4.120198e-01 3.820106e-01
## Cocktail.Naive_CD8_T_cells_NFkB            2.664262e-02 5.505388e-02
## Cocktail.Naive_CD8_T_cells_ERK             1.424804e-01 1.540346e-01
## Cocktail.Memory_CD8_T_cells_CREB           3.788877e-04 8.280178e-04
## Cocktail.Memory_CD8_T_cells_STAT5          1.652558e-02 1.919699e-02
## Cocktail.Memory_CD8_T_cells_p38            8.370742e-01 7.995565e-01
## Cocktail.Memory_CD8_T_cells_STAT1          4.291684e-01 3.189040e-01
## Cocktail.Memory_CD8_T_cells_STAT3          1.725063e-04 1.535046e-04
## Cocktail.Memory_CD8_T_cells_S6             2.328950e-04 2.050139e-03
## Cocktail.Memory_CD8_T_cells_MAPKAPK2       8.034781e-01 8.207947e-01
## Cocktail.Memory_CD8_T_cells_IkB            6.777275e-01 6.450120e-01
## Cocktail.Memory_CD8_T_cells_NFkB           5.919293e-03 2.342677e-02
## Cocktail.Memory_CD8_T_cells_ERK            4.384657e-03 1.068121e-02
## Cocktail.B_cells_CREB                      4.937880e-03 1.299845e-02
## Cocktail.B_cells_STAT5                     2.288309e-02 6.888140e-03
## Cocktail.B_cells_p38                       1.693435e-02 5.075257e-03
## Cocktail.B_cells_STAT1                     3.303124e-02 1.447228e-02
## Cocktail.B_cells_STAT3                     7.760841e-01 6.675445e-01
## Cocktail.B_cells_S6                        2.850547e-02 4.220920e-02
## Cocktail.B_cells_MAPKAPK2                  9.417264e-01 9.548476e-01
## Cocktail.B_cells_IkB                       9.206397e-01 9.230658e-01
## Cocktail.B_cells_NFkB                      3.614471e-01 3.758984e-01
## Cocktail.B_cells_ERK                       1.668044e-02 4.291246e-02
## Cocktail.Classical_monocytes_CREB          1.939082e-01 1.558125e-01
## Cocktail.Classical_monocytes_STAT5         9.342864e-01 8.922295e-01
## Cocktail.Classical_monocytes_p38           1.094087e-01 3.463008e-02
## Cocktail.Classical_monocytes_STAT1         2.841755e-08 7.789758e-07
## Cocktail.Classical_monocytes_STAT3         6.855633e-06 1.565196e-05
## Cocktail.Classical_monocytes_S6            1.246413e-01 1.264242e-01
## Cocktail.Classical_monocytes_MAPKAPK2      2.842675e-01 2.877560e-01
## Cocktail.Classical_monocytes_IkB           5.950901e-01 4.427354e-01
## Cocktail.Classical_monocytes_NFkB          4.523743e-01 3.357986e-01
## Cocktail.Classical_monocytes_ERK           5.187035e-01 4.689330e-01
## Cocktail.Nonclassical_monocytes_CREB       3.876510e-03 8.650712e-03
## Cocktail.Nonclassical_monocytes_STAT5      4.378046e-01 1.930798e-01
## Cocktail.Nonclassical_monocytes_p38        2.036744e-01 1.467368e-01
## Cocktail.Nonclassical_monocytes_STAT1      6.214642e-02 2.287062e-03
## Cocktail.Nonclassical_monocytes_STAT3      4.212228e-01 3.111970e-01
## Cocktail.Nonclassical_monocytes_S6         4.689136e-03 1.563354e-03
## Cocktail.Nonclassical_monocytes_MAPKAPK2   5.149079e-02 2.379052e-02
## Cocktail.Nonclassical_monocytes_IkB        6.351573e-02 9.667225e-02
## Cocktail.Nonclassical_monocytes_NFkB       7.876686e-01 8.073924e-01
## Cocktail.Nonclassical_monocytes_ERK        1.744932e-01 1.139294e-01
## Cocktail.cDCs_CREB                         1.263203e-01 9.709402e-02
## Cocktail.cDCs_STAT5                        7.647796e-01 6.162087e-01
## Cocktail.cDCs_p38                          1.282695e-01 4.313086e-02
## Cocktail.cDCs_STAT1                        5.664502e-08 8.851559e-07
## Cocktail.cDCs_STAT3                        1.307988e-05 1.848289e-05
## Cocktail.cDCs_S6                           1.067419e-01 1.070221e-01
## Cocktail.cDCs_MAPKAPK2                     2.207743e-01 2.359625e-01
## Cocktail.cDCs_IkB                          7.626307e-01 6.272978e-01
## Cocktail.cDCs_NFkB                         3.851362e-01 2.563916e-01
## Cocktail.cDCs_ERK                          6.458639e-01 6.060402e-01
## Cocktail.pDCs_CREB                         1.603890e-01 2.980323e-02
## Cocktail.pDCs_STAT5                        6.491161e-04 2.011305e-04
## Cocktail.pDCs_p38                          4.607230e-02 3.198227e-02
## Cocktail.pDCs_STAT1                        7.492047e-04 1.716831e-03
## Cocktail.pDCs_STAT3                        3.302022e-03 1.456874e-03
## Cocktail.pDCs_S6                           7.388744e-01 6.015124e-01
## Cocktail.pDCs_MAPKAPK2                     3.158995e-01 2.974472e-01
## Cocktail.pDCs_IkB                          6.574854e-01 6.514537e-01
## Cocktail.pDCs_NFkB                         6.359373e-01 5.050466e-01
## Cocktail.pDCs_ERK                          1.171944e-02 1.017372e-02
## Cocktail.Th1_T_cells_CREB                  5.680841e-01 5.316317e-01
## Cocktail.Th1_T_cells_STAT5                 2.787419e-02 2.875396e-02
## Cocktail.Th1_T_cells_p38                   9.392599e-02 6.677759e-02
## Cocktail.Th1_T_cells_STAT1                 3.925863e-01 3.639653e-01
## Cocktail.Th1_T_cells_STAT3                 4.461670e-02 4.337438e-02
## Cocktail.Th1_T_cells_S6                    2.304310e-01 2.303534e-01
## Cocktail.Th1_T_cells_MAPKAPK2              1.196136e-01 1.665136e-01
## Cocktail.Th1_T_cells_IkB                   4.121526e-02 5.902332e-02
## Cocktail.Th1_T_cells_NFkB                  5.955223e-01 5.593781e-01
## Cocktail.Th1_T_cells_ERK                   1.307151e-03 5.133213e-03
## Cocktail.Intermediate_monocytes_CREB       1.127104e-03 1.116942e-03
## Cocktail.Intermediate_monocytes_STAT5      4.433319e-01 3.608981e-01
## Cocktail.Intermediate_monocytes_p38        6.886138e-01 6.699712e-01
## Cocktail.Intermediate_monocytes_STAT1      3.336481e-05 6.527878e-05
## Cocktail.Intermediate_monocytes_STAT3      2.230762e-03 2.962565e-03
## Cocktail.Intermediate_monocytes_S6         1.042892e-02 3.125920e-03
## Cocktail.Intermediate_monocytes_MAPKAPK2   2.393513e-03 1.320800e-03
## Cocktail.Intermediate_monocytes_IkB        4.146176e-01 2.146026e-01
## Cocktail.Intermediate_monocytes_NFkB       5.150615e-01 4.151476e-01
## Cocktail.Intermediate_monocytes_ERK        5.451841e-01 4.992171e-01
## Cocktail.MDSCs_CREB                        2.312746e-01 2.156919e-01
## Cocktail.MDSCs_STAT5                       5.408239e-01 5.439189e-01
## Cocktail.MDSCs_p38                         3.518591e-01 2.211300e-01
## Cocktail.MDSCs_STAT1                       9.750655e-03 6.265596e-03
## Cocktail.MDSCs_STAT3                       2.901321e-03 9.500139e-04
## Cocktail.MDSCs_S6                          2.378545e-01 2.516392e-01
## Cocktail.MDSCs_MAPKAPK2                    3.387969e-01 3.139538e-01
## Cocktail.MDSCs_IkB                         5.414387e-02 8.515345e-02
## Cocktail.MDSCs_NFkB                        6.702804e-01 6.050355e-01
## Cocktail.MDSCs_ERK                         3.005668e-01 3.186393e-01
## Cocktail.Tregs_CREB                        4.747852e-01 4.855306e-01
## Cocktail.Tregs_STAT5                       4.776483e-02 5.753623e-02
## Cocktail.Tregs_p38                         4.895483e-01 8.439426e-02
## Cocktail.Tregs_STAT1                       3.442452e-05 4.924785e-06
## Cocktail.Tregs_STAT3                       3.484357e-01 2.346570e-01
## Cocktail.Tregs_S6                          4.160392e-01 3.081049e-01
## Cocktail.Tregs_MAPKAPK2                    2.261250e-02 3.508891e-02
## Cocktail.Tregs_IkB                         7.806999e-01 8.237691e-01
## Cocktail.Tregs_NFkB                        1.167344e-01 1.068907e-01
## Cocktail.Tregs_ERK                         7.439415e-02 8.855175e-02
## Cocktail.CD56lo_NK_cells_CREB              8.455179e-03 1.494249e-02
## Cocktail.CD56lo_NK_cells_STAT5             3.063707e-01 2.485959e-01
## Cocktail.CD56lo_NK_cells_p38               2.620391e-02 1.703064e-02
## Cocktail.CD56lo_NK_cells_STAT1             2.076970e-06 1.029504e-05
## Cocktail.CD56lo_NK_cells_STAT3             4.151752e-03 1.171908e-03
## Cocktail.CD56lo_NK_cells_S6                1.339833e-02 2.573930e-03
## Cocktail.CD56lo_NK_cells_MAPKAPK2          1.053266e-01 9.598332e-02
## Cocktail.CD56lo_NK_cells_IkB               8.743075e-01 8.746084e-01
## Cocktail.CD56lo_NK_cells_NFkB              4.140349e-02 7.344984e-02
## Cocktail.CD56lo_NK_cells_ERK               8.315580e-03 6.847928e-03
## Cocktail.CD56hi_NK_cells_CREB              5.888640e-01 6.111748e-01
## Cocktail.CD56hi_NK_cells_STAT5             6.212979e-02 6.115063e-02
## Cocktail.CD56hi_NK_cells_p38               1.550163e-01 1.215461e-01
## Cocktail.CD56hi_NK_cells_STAT1             3.337674e-06 2.983835e-05
## Cocktail.CD56hi_NK_cells_STAT3             1.055475e-01 7.141878e-02
## Cocktail.CD56hi_NK_cells_S6                9.356835e-01 9.286171e-01
## Cocktail.CD56hi_NK_cells_MAPKAPK2          2.028708e-05 1.203565e-04
## Cocktail.CD56hi_NK_cells_IkB               6.147455e-01 5.801014e-01
## Cocktail.CD56hi_NK_cells_NFkB              8.730336e-01 8.761052e-01
## Cocktail.CD56hi_NK_cells_ERK               3.710699e-01 2.603457e-01
## Cocktail.gd_T_cells_CREB                   1.109352e-02 3.715116e-02
## Cocktail.gd_T_cells_STAT5                  5.808676e-04 8.337238e-04
## Cocktail.gd_T_cells_p38                    3.567935e-01 3.415657e-01
## Cocktail.gd_T_cells_STAT1                  5.858359e-03 1.132979e-03
## Cocktail.gd_T_cells_STAT3                  1.942003e-02 2.531648e-03
## Cocktail.gd_T_cells_S6                     8.956167e-03 3.901922e-02
## Cocktail.gd_T_cells_MAPKAPK2               4.219607e-01 4.677677e-01
## Cocktail.gd_T_cells_IkB                    8.630195e-01 8.739116e-01
## Cocktail.gd_T_cells_NFkB                   1.359771e-01 1.610754e-01
## Cocktail.gd_T_cells_ERK                    1.907227e-02 4.130626e-02
## Cocktail.Memory_CD4_T_cells_CREB           3.344587e-01 4.220362e-01
## Cocktail.Memory_CD4_T_cells_STAT5          1.739381e-04 1.217589e-03
## Cocktail.Memory_CD4_T_cells_p38            9.918864e-01 9.814792e-01
## Cocktail.Memory_CD4_T_cells_STAT1          3.296811e-03 3.919114e-04
## Cocktail.Memory_CD4_T_cells_STAT3          6.549891e-01 6.106366e-01
## Cocktail.Memory_CD4_T_cells_S6             8.373510e-03 3.548889e-03
## Cocktail.Memory_CD4_T_cells_MAPKAPK2       1.485663e-02 4.008193e-02
## Cocktail.Memory_CD4_T_cells_IkB            8.382569e-01 8.207364e-01
## Cocktail.Memory_CD4_T_cells_NFkB           1.989691e-02 1.709443e-02
## Cocktail.Memory_CD4_T_cells_ERK            4.191026e-01 4.036851e-01
##                                          Significance_Bonferroni
## LPS.Granulocytes_CREB                            Not significant
## LPS.Granulocytes_STAT5                           Not significant
## LPS.Granulocytes_p38                             Not significant
## LPS.Granulocytes_STAT1                           Not significant
## LPS.Granulocytes_STAT3                           Not significant
## LPS.Granulocytes_S6                              Not significant
## LPS.Granulocytes_MAPKAPK2                        Not significant
## LPS.Granulocytes_IkB                             Not significant
## LPS.Granulocytes_NFkB                                       Both
## LPS.Granulocytes_ERK                             Not significant
## LPS.CD8_T_cells_CREB                             Not significant
## LPS.CD8_T_cells_STAT5                            Not significant
## LPS.CD8_T_cells_p38                              Not significant
## LPS.CD8_T_cells_STAT1                            Not significant
## LPS.CD8_T_cells_STAT3                            Not significant
## LPS.CD8_T_cells_S6                               Not significant
## LPS.CD8_T_cells_MAPKAPK2                         Not significant
## LPS.CD8_T_cells_IkB                              Not significant
## LPS.CD8_T_cells_NFkB                             Not significant
## LPS.CD8_T_cells_ERK                              Not significant
## LPS.CD4_T_cells_CREB                             Not significant
## LPS.CD4_T_cells_STAT5                            Not significant
## LPS.CD4_T_cells_p38                              Not significant
## LPS.CD4_T_cells_STAT1                            Not significant
## LPS.CD4_T_cells_STAT3                            Not significant
## LPS.CD4_T_cells_S6                               Not significant
## LPS.CD4_T_cells_MAPKAPK2                         Not significant
## LPS.CD4_T_cells_IkB                              Not significant
## LPS.CD4_T_cells_NFkB                             Not significant
## LPS.CD4_T_cells_ERK                              Not significant
## LPS.Naive_CD4_T_cells_CREB                       Not significant
## LPS.Naive_CD4_T_cells_STAT5                      Not significant
## LPS.Naive_CD4_T_cells_p38                        Not significant
## LPS.Naive_CD4_T_cells_STAT1                      Not significant
## LPS.Naive_CD4_T_cells_STAT3                      Not significant
## LPS.Naive_CD4_T_cells_S6                         Not significant
## LPS.Naive_CD4_T_cells_MAPKAPK2                   Not significant
## LPS.Naive_CD4_T_cells_IkB                        Not significant
## LPS.Naive_CD4_T_cells_NFkB                       Not significant
## LPS.Naive_CD4_T_cells_ERK                        Not significant
## LPS.Naive_CD8_T_cells_CREB                       Not significant
## LPS.Naive_CD8_T_cells_STAT5                      Not significant
## LPS.Naive_CD8_T_cells_p38                        Not significant
## LPS.Naive_CD8_T_cells_STAT1                      Not significant
## LPS.Naive_CD8_T_cells_STAT3                      Not significant
## LPS.Naive_CD8_T_cells_S6                         Not significant
## LPS.Naive_CD8_T_cells_MAPKAPK2                   Not significant
## LPS.Naive_CD8_T_cells_IkB                        Not significant
## LPS.Naive_CD8_T_cells_NFkB                       Not significant
## LPS.Naive_CD8_T_cells_ERK                        Not significant
## LPS.Memory_CD8_T_cells_CREB                      Not significant
## LPS.Memory_CD8_T_cells_STAT5                     Not significant
## LPS.Memory_CD8_T_cells_p38                       Not significant
## LPS.Memory_CD8_T_cells_STAT1                     Not significant
## LPS.Memory_CD8_T_cells_STAT3                     Not significant
## LPS.Memory_CD8_T_cells_S6                            Paired only
## LPS.Memory_CD8_T_cells_MAPKAPK2                  Not significant
## LPS.Memory_CD8_T_cells_IkB                       Not significant
## LPS.Memory_CD8_T_cells_NFkB                      Not significant
## LPS.Memory_CD8_T_cells_ERK                       Not significant
## LPS.B_cells_CREB                                 Not significant
## LPS.B_cells_STAT5                                Not significant
## LPS.B_cells_p38                                  Not significant
## LPS.B_cells_STAT1                                Not significant
## LPS.B_cells_STAT3                                Not significant
## LPS.B_cells_S6                                   Not significant
## LPS.B_cells_MAPKAPK2                             Not significant
## LPS.B_cells_IkB                                  Not significant
## LPS.B_cells_NFkB                                 Not significant
## LPS.B_cells_ERK                                  Not significant
## LPS.Classical_monocytes_CREB                     Not significant
## LPS.Classical_monocytes_STAT5                    Not significant
## LPS.Classical_monocytes_p38                      Not significant
## LPS.Classical_monocytes_STAT1                    Not significant
## LPS.Classical_monocytes_STAT3                    Not significant
## LPS.Classical_monocytes_S6                       Not significant
## LPS.Classical_monocytes_MAPKAPK2                 Not significant
## LPS.Classical_monocytes_IkB                      Not significant
## LPS.Classical_monocytes_NFkB                     Not significant
## LPS.Classical_monocytes_ERK                        Unpaired only
## LPS.Nonclassical_monocytes_CREB                  Not significant
## LPS.Nonclassical_monocytes_STAT5                 Not significant
## LPS.Nonclassical_monocytes_p38                   Not significant
## LPS.Nonclassical_monocytes_STAT1                 Not significant
## LPS.Nonclassical_monocytes_STAT3                 Not significant
## LPS.Nonclassical_monocytes_S6                    Not significant
## LPS.Nonclassical_monocytes_MAPKAPK2              Not significant
## LPS.Nonclassical_monocytes_IkB                   Not significant
## LPS.Nonclassical_monocytes_NFkB                  Not significant
## LPS.Nonclassical_monocytes_ERK                   Not significant
## LPS.cDCs_CREB                                    Not significant
## LPS.cDCs_STAT5                                   Not significant
## LPS.cDCs_p38                                     Not significant
## LPS.cDCs_STAT1                                   Not significant
## LPS.cDCs_STAT3                                   Not significant
## LPS.cDCs_S6                                      Not significant
## LPS.cDCs_MAPKAPK2                                Not significant
## LPS.cDCs_IkB                                     Not significant
## LPS.cDCs_NFkB                                    Not significant
## LPS.cDCs_ERK                                       Unpaired only
## LPS.pDCs_CREB                                    Not significant
## LPS.pDCs_STAT5                                   Not significant
## LPS.pDCs_p38                                     Not significant
## LPS.pDCs_STAT1                                   Not significant
## LPS.pDCs_STAT3                                   Not significant
## LPS.pDCs_S6                                      Not significant
## LPS.pDCs_MAPKAPK2                                Not significant
## LPS.pDCs_IkB                                     Not significant
## LPS.pDCs_NFkB                                    Not significant
## LPS.pDCs_ERK                                     Not significant
## LPS.Th1_T_cells_CREB                             Not significant
## LPS.Th1_T_cells_STAT5                            Not significant
## LPS.Th1_T_cells_p38                              Not significant
## LPS.Th1_T_cells_STAT1                            Not significant
## LPS.Th1_T_cells_STAT3                            Not significant
## LPS.Th1_T_cells_S6                               Not significant
## LPS.Th1_T_cells_MAPKAPK2                         Not significant
## LPS.Th1_T_cells_IkB                              Not significant
## LPS.Th1_T_cells_NFkB                             Not significant
## LPS.Th1_T_cells_ERK                              Not significant
## LPS.Intermediate_monocytes_CREB                  Not significant
## LPS.Intermediate_monocytes_STAT5                 Not significant
## LPS.Intermediate_monocytes_p38                   Not significant
## LPS.Intermediate_monocytes_STAT1                 Not significant
## LPS.Intermediate_monocytes_STAT3                 Not significant
## LPS.Intermediate_monocytes_S6                    Not significant
## LPS.Intermediate_monocytes_MAPKAPK2              Not significant
## LPS.Intermediate_monocytes_IkB                   Not significant
## LPS.Intermediate_monocytes_NFkB                  Not significant
## LPS.Intermediate_monocytes_ERK                   Not significant
## LPS.MDSCs_CREB                                   Not significant
## LPS.MDSCs_STAT5                                  Not significant
## LPS.MDSCs_p38                                    Not significant
## LPS.MDSCs_STAT1                                  Not significant
## LPS.MDSCs_STAT3                                  Not significant
## LPS.MDSCs_S6                                     Not significant
## LPS.MDSCs_MAPKAPK2                               Not significant
## LPS.MDSCs_IkB                                    Not significant
## LPS.MDSCs_NFkB                                   Not significant
## LPS.MDSCs_ERK                                    Not significant
## LPS.Tregs_CREB                                   Not significant
## LPS.Tregs_STAT5                                  Not significant
## LPS.Tregs_p38                                    Not significant
## LPS.Tregs_STAT1                                  Not significant
## LPS.Tregs_STAT3                                  Not significant
## LPS.Tregs_S6                                     Not significant
## LPS.Tregs_MAPKAPK2                               Not significant
## LPS.Tregs_IkB                                    Not significant
## LPS.Tregs_NFkB                                   Not significant
## LPS.Tregs_ERK                                    Not significant
## LPS.CD56lo_NK_cells_CREB                           Unpaired only
## LPS.CD56lo_NK_cells_STAT5                        Not significant
## LPS.CD56lo_NK_cells_p38                          Not significant
## LPS.CD56lo_NK_cells_STAT1                        Not significant
## LPS.CD56lo_NK_cells_STAT3                        Not significant
## LPS.CD56lo_NK_cells_S6                           Not significant
## LPS.CD56lo_NK_cells_MAPKAPK2                     Not significant
## LPS.CD56lo_NK_cells_IkB                          Not significant
## LPS.CD56lo_NK_cells_NFkB                         Not significant
## LPS.CD56lo_NK_cells_ERK                          Not significant
## LPS.CD56hi_NK_cells_CREB                         Not significant
## LPS.CD56hi_NK_cells_STAT5                        Not significant
## LPS.CD56hi_NK_cells_p38                          Not significant
## LPS.CD56hi_NK_cells_STAT1                        Not significant
## LPS.CD56hi_NK_cells_STAT3                        Not significant
## LPS.CD56hi_NK_cells_S6                           Not significant
## LPS.CD56hi_NK_cells_MAPKAPK2                     Not significant
## LPS.CD56hi_NK_cells_IkB                          Not significant
## LPS.CD56hi_NK_cells_NFkB                         Not significant
## LPS.CD56hi_NK_cells_ERK                          Not significant
## LPS.gd_T_cells_CREB                              Not significant
## LPS.gd_T_cells_STAT5                             Not significant
## LPS.gd_T_cells_p38                               Not significant
## LPS.gd_T_cells_STAT1                             Not significant
## LPS.gd_T_cells_STAT3                             Not significant
## LPS.gd_T_cells_S6                                Not significant
## LPS.gd_T_cells_MAPKAPK2                          Not significant
## LPS.gd_T_cells_IkB                               Not significant
## LPS.gd_T_cells_NFkB                              Not significant
## LPS.gd_T_cells_ERK                               Not significant
## LPS.Memory_CD4_T_cells_CREB                      Not significant
## LPS.Memory_CD4_T_cells_STAT5                     Not significant
## LPS.Memory_CD4_T_cells_p38                       Not significant
## LPS.Memory_CD4_T_cells_STAT1                     Not significant
## LPS.Memory_CD4_T_cells_STAT3                     Not significant
## LPS.Memory_CD4_T_cells_S6                        Not significant
## LPS.Memory_CD4_T_cells_MAPKAPK2                  Not significant
## LPS.Memory_CD4_T_cells_IkB                       Not significant
## LPS.Memory_CD4_T_cells_NFkB                      Not significant
## LPS.Memory_CD4_T_cells_ERK                       Not significant
## Cocktail.Granulocytes_CREB                       Not significant
## Cocktail.Granulocytes_STAT5                      Not significant
## Cocktail.Granulocytes_p38                        Not significant
## Cocktail.Granulocytes_STAT1                      Not significant
## Cocktail.Granulocytes_STAT3                      Not significant
## Cocktail.Granulocytes_S6                         Not significant
## Cocktail.Granulocytes_MAPKAPK2                   Not significant
## Cocktail.Granulocytes_IkB                        Not significant
## Cocktail.Granulocytes_NFkB                       Not significant
## Cocktail.Granulocytes_ERK                        Not significant
## Cocktail.CD8_T_cells_CREB                        Not significant
## Cocktail.CD8_T_cells_STAT5                         Unpaired only
## Cocktail.CD8_T_cells_p38                         Not significant
## Cocktail.CD8_T_cells_STAT1                       Not significant
## Cocktail.CD8_T_cells_STAT3                       Not significant
## Cocktail.CD8_T_cells_S6                          Not significant
## Cocktail.CD8_T_cells_MAPKAPK2                    Not significant
## Cocktail.CD8_T_cells_IkB                         Not significant
## Cocktail.CD8_T_cells_NFkB                        Not significant
## Cocktail.CD8_T_cells_ERK                         Not significant
## Cocktail.CD4_T_cells_CREB                        Not significant
## Cocktail.CD4_T_cells_STAT5                         Unpaired only
## Cocktail.CD4_T_cells_p38                         Not significant
## Cocktail.CD4_T_cells_STAT1                                  Both
## Cocktail.CD4_T_cells_STAT3                       Not significant
## Cocktail.CD4_T_cells_S6                          Not significant
## Cocktail.CD4_T_cells_MAPKAPK2                    Not significant
## Cocktail.CD4_T_cells_IkB                         Not significant
## Cocktail.CD4_T_cells_NFkB                        Not significant
## Cocktail.CD4_T_cells_ERK                         Not significant
## Cocktail.Naive_CD4_T_cells_CREB                  Not significant
## Cocktail.Naive_CD4_T_cells_STAT5                            Both
## Cocktail.Naive_CD4_T_cells_p38                   Not significant
## Cocktail.Naive_CD4_T_cells_STAT1                            Both
## Cocktail.Naive_CD4_T_cells_STAT3                 Not significant
## Cocktail.Naive_CD4_T_cells_S6                    Not significant
## Cocktail.Naive_CD4_T_cells_MAPKAPK2              Not significant
## Cocktail.Naive_CD4_T_cells_IkB                   Not significant
## Cocktail.Naive_CD4_T_cells_NFkB                  Not significant
## Cocktail.Naive_CD4_T_cells_ERK                   Not significant
## Cocktail.Naive_CD8_T_cells_CREB                  Not significant
## Cocktail.Naive_CD8_T_cells_STAT5                            Both
## Cocktail.Naive_CD8_T_cells_p38                   Not significant
## Cocktail.Naive_CD8_T_cells_STAT1                 Not significant
## Cocktail.Naive_CD8_T_cells_STAT3                 Not significant
## Cocktail.Naive_CD8_T_cells_S6                    Not significant
## Cocktail.Naive_CD8_T_cells_MAPKAPK2              Not significant
## Cocktail.Naive_CD8_T_cells_IkB                   Not significant
## Cocktail.Naive_CD8_T_cells_NFkB                  Not significant
## Cocktail.Naive_CD8_T_cells_ERK                   Not significant
## Cocktail.Memory_CD8_T_cells_CREB                 Not significant
## Cocktail.Memory_CD8_T_cells_STAT5                Not significant
## Cocktail.Memory_CD8_T_cells_p38                  Not significant
## Cocktail.Memory_CD8_T_cells_STAT1                Not significant
## Cocktail.Memory_CD8_T_cells_STAT3                Not significant
## Cocktail.Memory_CD8_T_cells_S6                   Not significant
## Cocktail.Memory_CD8_T_cells_MAPKAPK2             Not significant
## Cocktail.Memory_CD8_T_cells_IkB                  Not significant
## Cocktail.Memory_CD8_T_cells_NFkB                 Not significant
## Cocktail.Memory_CD8_T_cells_ERK                  Not significant
## Cocktail.B_cells_CREB                            Not significant
## Cocktail.B_cells_STAT5                           Not significant
## Cocktail.B_cells_p38                             Not significant
## Cocktail.B_cells_STAT1                           Not significant
## Cocktail.B_cells_STAT3                           Not significant
## Cocktail.B_cells_S6                              Not significant
## Cocktail.B_cells_MAPKAPK2                        Not significant
## Cocktail.B_cells_IkB                             Not significant
## Cocktail.B_cells_NFkB                            Not significant
## Cocktail.B_cells_ERK                             Not significant
## Cocktail.Classical_monocytes_CREB                Not significant
## Cocktail.Classical_monocytes_STAT5               Not significant
## Cocktail.Classical_monocytes_p38                 Not significant
## Cocktail.Classical_monocytes_STAT1                          Both
## Cocktail.Classical_monocytes_STAT3                          Both
## Cocktail.Classical_monocytes_S6                  Not significant
## Cocktail.Classical_monocytes_MAPKAPK2            Not significant
## Cocktail.Classical_monocytes_IkB                 Not significant
## Cocktail.Classical_monocytes_NFkB                Not significant
## Cocktail.Classical_monocytes_ERK                 Not significant
## Cocktail.Nonclassical_monocytes_CREB             Not significant
## Cocktail.Nonclassical_monocytes_STAT5            Not significant
## Cocktail.Nonclassical_monocytes_p38              Not significant
## Cocktail.Nonclassical_monocytes_STAT1            Not significant
## Cocktail.Nonclassical_monocytes_STAT3            Not significant
## Cocktail.Nonclassical_monocytes_S6               Not significant
## Cocktail.Nonclassical_monocytes_MAPKAPK2         Not significant
## Cocktail.Nonclassical_monocytes_IkB              Not significant
## Cocktail.Nonclassical_monocytes_NFkB             Not significant
## Cocktail.Nonclassical_monocytes_ERK              Not significant
## Cocktail.cDCs_CREB                               Not significant
## Cocktail.cDCs_STAT5                              Not significant
## Cocktail.cDCs_p38                                Not significant
## Cocktail.cDCs_STAT1                                         Both
## Cocktail.cDCs_STAT3                                         Both
## Cocktail.cDCs_S6                                 Not significant
## Cocktail.cDCs_MAPKAPK2                           Not significant
## Cocktail.cDCs_IkB                                Not significant
## Cocktail.cDCs_NFkB                               Not significant
## Cocktail.cDCs_ERK                                Not significant
## Cocktail.pDCs_CREB                               Not significant
## Cocktail.pDCs_STAT5                              Not significant
## Cocktail.pDCs_p38                                Not significant
## Cocktail.pDCs_STAT1                              Not significant
## Cocktail.pDCs_STAT3                              Not significant
## Cocktail.pDCs_S6                                 Not significant
## Cocktail.pDCs_MAPKAPK2                           Not significant
## Cocktail.pDCs_IkB                                Not significant
## Cocktail.pDCs_NFkB                               Not significant
## Cocktail.pDCs_ERK                                Not significant
## Cocktail.Th1_T_cells_CREB                        Not significant
## Cocktail.Th1_T_cells_STAT5                       Not significant
## Cocktail.Th1_T_cells_p38                         Not significant
## Cocktail.Th1_T_cells_STAT1                       Not significant
## Cocktail.Th1_T_cells_STAT3                       Not significant
## Cocktail.Th1_T_cells_S6                          Not significant
## Cocktail.Th1_T_cells_MAPKAPK2                    Not significant
## Cocktail.Th1_T_cells_IkB                         Not significant
## Cocktail.Th1_T_cells_NFkB                        Not significant
## Cocktail.Th1_T_cells_ERK                         Not significant
## Cocktail.Intermediate_monocytes_CREB             Not significant
## Cocktail.Intermediate_monocytes_STAT5            Not significant
## Cocktail.Intermediate_monocytes_p38              Not significant
## Cocktail.Intermediate_monocytes_STAT1                       Both
## Cocktail.Intermediate_monocytes_STAT3            Not significant
## Cocktail.Intermediate_monocytes_S6               Not significant
## Cocktail.Intermediate_monocytes_MAPKAPK2         Not significant
## Cocktail.Intermediate_monocytes_IkB              Not significant
## Cocktail.Intermediate_monocytes_NFkB             Not significant
## Cocktail.Intermediate_monocytes_ERK              Not significant
## Cocktail.MDSCs_CREB                              Not significant
## Cocktail.MDSCs_STAT5                             Not significant
## Cocktail.MDSCs_p38                               Not significant
## Cocktail.MDSCs_STAT1                             Not significant
## Cocktail.MDSCs_STAT3                             Not significant
## Cocktail.MDSCs_S6                                Not significant
## Cocktail.MDSCs_MAPKAPK2                          Not significant
## Cocktail.MDSCs_IkB                               Not significant
## Cocktail.MDSCs_NFkB                              Not significant
## Cocktail.MDSCs_ERK                               Not significant
## Cocktail.Tregs_CREB                              Not significant
## Cocktail.Tregs_STAT5                             Not significant
## Cocktail.Tregs_p38                               Not significant
## Cocktail.Tregs_STAT1                                        Both
## Cocktail.Tregs_STAT3                             Not significant
## Cocktail.Tregs_S6                                Not significant
## Cocktail.Tregs_MAPKAPK2                          Not significant
## Cocktail.Tregs_IkB                               Not significant
## Cocktail.Tregs_NFkB                              Not significant
## Cocktail.Tregs_ERK                               Not significant
## Cocktail.CD56lo_NK_cells_CREB                    Not significant
## Cocktail.CD56lo_NK_cells_STAT5                   Not significant
## Cocktail.CD56lo_NK_cells_p38                     Not significant
## Cocktail.CD56lo_NK_cells_STAT1                              Both
## Cocktail.CD56lo_NK_cells_STAT3                   Not significant
## Cocktail.CD56lo_NK_cells_S6                      Not significant
## Cocktail.CD56lo_NK_cells_MAPKAPK2                Not significant
## Cocktail.CD56lo_NK_cells_IkB                     Not significant
## Cocktail.CD56lo_NK_cells_NFkB                    Not significant
## Cocktail.CD56lo_NK_cells_ERK                     Not significant
## Cocktail.CD56hi_NK_cells_CREB                    Not significant
## Cocktail.CD56hi_NK_cells_STAT5                   Not significant
## Cocktail.CD56hi_NK_cells_p38                     Not significant
## Cocktail.CD56hi_NK_cells_STAT1                              Both
## Cocktail.CD56hi_NK_cells_STAT3                   Not significant
## Cocktail.CD56hi_NK_cells_S6                      Not significant
## Cocktail.CD56hi_NK_cells_MAPKAPK2                           Both
## Cocktail.CD56hi_NK_cells_IkB                     Not significant
## Cocktail.CD56hi_NK_cells_NFkB                    Not significant
## Cocktail.CD56hi_NK_cells_ERK                     Not significant
## Cocktail.gd_T_cells_CREB                         Not significant
## Cocktail.gd_T_cells_STAT5                        Not significant
## Cocktail.gd_T_cells_p38                          Not significant
## Cocktail.gd_T_cells_STAT1                        Not significant
## Cocktail.gd_T_cells_STAT3                        Not significant
## Cocktail.gd_T_cells_S6                           Not significant
## Cocktail.gd_T_cells_MAPKAPK2                     Not significant
## Cocktail.gd_T_cells_IkB                          Not significant
## Cocktail.gd_T_cells_NFkB                         Not significant
## Cocktail.gd_T_cells_ERK                          Not significant
## Cocktail.Memory_CD4_T_cells_CREB                 Not significant
## Cocktail.Memory_CD4_T_cells_STAT5                Not significant
## Cocktail.Memory_CD4_T_cells_p38                  Not significant
## Cocktail.Memory_CD4_T_cells_STAT1                Not significant
## Cocktail.Memory_CD4_T_cells_STAT3                Not significant
## Cocktail.Memory_CD4_T_cells_S6                   Not significant
## Cocktail.Memory_CD4_T_cells_MAPKAPK2             Not significant
## Cocktail.Memory_CD4_T_cells_IkB                  Not significant
## Cocktail.Memory_CD4_T_cells_NFkB                 Not significant
## Cocktail.Memory_CD4_T_cells_ERK                  Not significant
##                                          Significance_SAM
## LPS.Granulocytes_CREB                                Both
## LPS.Granulocytes_STAT5                    Not significant
## LPS.Granulocytes_p38                                 Both
## LPS.Granulocytes_STAT1                               Both
## LPS.Granulocytes_STAT3                    Not significant
## LPS.Granulocytes_S6                       Not significant
## LPS.Granulocytes_MAPKAPK2                            Both
## LPS.Granulocytes_IkB                      Not significant
## LPS.Granulocytes_NFkB                                Both
## LPS.Granulocytes_ERK                      Not significant
## LPS.CD8_T_cells_CREB                      Not significant
## LPS.CD8_T_cells_STAT5                     Not significant
## LPS.CD8_T_cells_p38                       Not significant
## LPS.CD8_T_cells_STAT1                     Not significant
## LPS.CD8_T_cells_STAT3                     Not significant
## LPS.CD8_T_cells_S6                        Not significant
## LPS.CD8_T_cells_MAPKAPK2                  Not significant
## LPS.CD8_T_cells_IkB                       Not significant
## LPS.CD8_T_cells_NFkB                      Not significant
## LPS.CD8_T_cells_ERK                       Not significant
## LPS.CD4_T_cells_CREB                      Not significant
## LPS.CD4_T_cells_STAT5                     Not significant
## LPS.CD4_T_cells_p38                       Not significant
## LPS.CD4_T_cells_STAT1                     Not significant
## LPS.CD4_T_cells_STAT3                     Not significant
## LPS.CD4_T_cells_S6                        Not significant
## LPS.CD4_T_cells_MAPKAPK2                  Not significant
## LPS.CD4_T_cells_IkB                       Not significant
## LPS.CD4_T_cells_NFkB                      Not significant
## LPS.CD4_T_cells_ERK                       Not significant
## LPS.Naive_CD4_T_cells_CREB                Not significant
## LPS.Naive_CD4_T_cells_STAT5               Not significant
## LPS.Naive_CD4_T_cells_p38                 Not significant
## LPS.Naive_CD4_T_cells_STAT1               Not significant
## LPS.Naive_CD4_T_cells_STAT3               Not significant
## LPS.Naive_CD4_T_cells_S6                  Not significant
## LPS.Naive_CD4_T_cells_MAPKAPK2            Not significant
## LPS.Naive_CD4_T_cells_IkB                   Unpaired only
## LPS.Naive_CD4_T_cells_NFkB                Not significant
## LPS.Naive_CD4_T_cells_ERK                            Both
## LPS.Naive_CD8_T_cells_CREB                Not significant
## LPS.Naive_CD8_T_cells_STAT5               Not significant
## LPS.Naive_CD8_T_cells_p38                 Not significant
## LPS.Naive_CD8_T_cells_STAT1               Not significant
## LPS.Naive_CD8_T_cells_STAT3               Not significant
## LPS.Naive_CD8_T_cells_S6                  Not significant
## LPS.Naive_CD8_T_cells_MAPKAPK2            Not significant
## LPS.Naive_CD8_T_cells_IkB                   Unpaired only
## LPS.Naive_CD8_T_cells_NFkB                Not significant
## LPS.Naive_CD8_T_cells_ERK                 Not significant
## LPS.Memory_CD8_T_cells_CREB                          Both
## LPS.Memory_CD8_T_cells_STAT5              Not significant
## LPS.Memory_CD8_T_cells_p38                  Unpaired only
## LPS.Memory_CD8_T_cells_STAT1              Not significant
## LPS.Memory_CD8_T_cells_STAT3              Not significant
## LPS.Memory_CD8_T_cells_S6                            Both
## LPS.Memory_CD8_T_cells_MAPKAPK2           Not significant
## LPS.Memory_CD8_T_cells_IkB                Not significant
## LPS.Memory_CD8_T_cells_NFkB               Not significant
## LPS.Memory_CD8_T_cells_ERK                Not significant
## LPS.B_cells_CREB                          Not significant
## LPS.B_cells_STAT5                                    Both
## LPS.B_cells_p38                           Not significant
## LPS.B_cells_STAT1                         Not significant
## LPS.B_cells_STAT3                         Not significant
## LPS.B_cells_S6                              Unpaired only
## LPS.B_cells_MAPKAPK2                      Not significant
## LPS.B_cells_IkB                           Not significant
## LPS.B_cells_NFkB                          Not significant
## LPS.B_cells_ERK                                      Both
## LPS.Classical_monocytes_CREB              Not significant
## LPS.Classical_monocytes_STAT5             Not significant
## LPS.Classical_monocytes_p38               Not significant
## LPS.Classical_monocytes_STAT1             Not significant
## LPS.Classical_monocytes_STAT3             Not significant
## LPS.Classical_monocytes_S6                Not significant
## LPS.Classical_monocytes_MAPKAPK2                     Both
## LPS.Classical_monocytes_IkB               Not significant
## LPS.Classical_monocytes_NFkB              Not significant
## LPS.Classical_monocytes_ERK                          Both
## LPS.Nonclassical_monocytes_CREB                      Both
## LPS.Nonclassical_monocytes_STAT5          Not significant
## LPS.Nonclassical_monocytes_p38            Not significant
## LPS.Nonclassical_monocytes_STAT1          Not significant
## LPS.Nonclassical_monocytes_STAT3          Not significant
## LPS.Nonclassical_monocytes_S6                        Both
## LPS.Nonclassical_monocytes_MAPKAPK2       Not significant
## LPS.Nonclassical_monocytes_IkB            Not significant
## LPS.Nonclassical_monocytes_NFkB           Not significant
## LPS.Nonclassical_monocytes_ERK            Not significant
## LPS.cDCs_CREB                                        Both
## LPS.cDCs_STAT5                            Not significant
## LPS.cDCs_p38                                  Paired only
## LPS.cDCs_STAT1                            Not significant
## LPS.cDCs_STAT3                            Not significant
## LPS.cDCs_S6                                 Unpaired only
## LPS.cDCs_MAPKAPK2                                    Both
## LPS.cDCs_IkB                              Not significant
## LPS.cDCs_NFkB                             Not significant
## LPS.cDCs_ERK                                         Both
## LPS.pDCs_CREB                               Unpaired only
## LPS.pDCs_STAT5                            Not significant
## LPS.pDCs_p38                              Not significant
## LPS.pDCs_STAT1                            Not significant
## LPS.pDCs_STAT3                                       Both
## LPS.pDCs_S6                                          Both
## LPS.pDCs_MAPKAPK2                         Not significant
## LPS.pDCs_IkB                              Not significant
## LPS.pDCs_NFkB                             Not significant
## LPS.pDCs_ERK                                         Both
## LPS.Th1_T_cells_CREB                                 Both
## LPS.Th1_T_cells_STAT5                                Both
## LPS.Th1_T_cells_p38                                  Both
## LPS.Th1_T_cells_STAT1                                Both
## LPS.Th1_T_cells_STAT3                                Both
## LPS.Th1_T_cells_S6                                   Both
## LPS.Th1_T_cells_MAPKAPK2                             Both
## LPS.Th1_T_cells_IkB                                  Both
## LPS.Th1_T_cells_NFkB                      Not significant
## LPS.Th1_T_cells_ERK                                  Both
## LPS.Intermediate_monocytes_CREB                      Both
## LPS.Intermediate_monocytes_STAT5          Not significant
## LPS.Intermediate_monocytes_p38            Not significant
## LPS.Intermediate_monocytes_STAT1          Not significant
## LPS.Intermediate_monocytes_STAT3            Unpaired only
## LPS.Intermediate_monocytes_S6                        Both
## LPS.Intermediate_monocytes_MAPKAPK2       Not significant
## LPS.Intermediate_monocytes_IkB                Paired only
## LPS.Intermediate_monocytes_NFkB           Not significant
## LPS.Intermediate_monocytes_ERK                       Both
## LPS.MDSCs_CREB                            Not significant
## LPS.MDSCs_STAT5                           Not significant
## LPS.MDSCs_p38                             Not significant
## LPS.MDSCs_STAT1                           Not significant
## LPS.MDSCs_STAT3                           Not significant
## LPS.MDSCs_S6                              Not significant
## LPS.MDSCs_MAPKAPK2                        Not significant
## LPS.MDSCs_IkB                             Not significant
## LPS.MDSCs_NFkB                            Not significant
## LPS.MDSCs_ERK                             Not significant
## LPS.Tregs_CREB                                       Both
## LPS.Tregs_STAT5                           Not significant
## LPS.Tregs_p38                                        Both
## LPS.Tregs_STAT1                                      Both
## LPS.Tregs_STAT3                           Not significant
## LPS.Tregs_S6                              Not significant
## LPS.Tregs_MAPKAPK2                        Not significant
## LPS.Tregs_IkB                             Not significant
## LPS.Tregs_NFkB                            Not significant
## LPS.Tregs_ERK                                        Both
## LPS.CD56lo_NK_cells_CREB                             Both
## LPS.CD56lo_NK_cells_STAT5                 Not significant
## LPS.CD56lo_NK_cells_p38                   Not significant
## LPS.CD56lo_NK_cells_STAT1                   Unpaired only
## LPS.CD56lo_NK_cells_STAT3                 Not significant
## LPS.CD56lo_NK_cells_S6                    Not significant
## LPS.CD56lo_NK_cells_MAPKAPK2              Not significant
## LPS.CD56lo_NK_cells_IkB                   Not significant
## LPS.CD56lo_NK_cells_NFkB                  Not significant
## LPS.CD56lo_NK_cells_ERK                   Not significant
## LPS.CD56hi_NK_cells_CREB                             Both
## LPS.CD56hi_NK_cells_STAT5                 Not significant
## LPS.CD56hi_NK_cells_p38                   Not significant
## LPS.CD56hi_NK_cells_STAT1                 Not significant
## LPS.CD56hi_NK_cells_STAT3                 Not significant
## LPS.CD56hi_NK_cells_S6                    Not significant
## LPS.CD56hi_NK_cells_MAPKAPK2              Not significant
## LPS.CD56hi_NK_cells_IkB                   Not significant
## LPS.CD56hi_NK_cells_NFkB                  Not significant
## LPS.CD56hi_NK_cells_ERK                              Both
## LPS.gd_T_cells_CREB                       Not significant
## LPS.gd_T_cells_STAT5                      Not significant
## LPS.gd_T_cells_p38                        Not significant
## LPS.gd_T_cells_STAT1                      Not significant
## LPS.gd_T_cells_STAT3                      Not significant
## LPS.gd_T_cells_S6                           Unpaired only
## LPS.gd_T_cells_MAPKAPK2                   Not significant
## LPS.gd_T_cells_IkB                        Not significant
## LPS.gd_T_cells_NFkB                       Not significant
## LPS.gd_T_cells_ERK                        Not significant
## LPS.Memory_CD4_T_cells_CREB               Not significant
## LPS.Memory_CD4_T_cells_STAT5              Not significant
## LPS.Memory_CD4_T_cells_p38                           Both
## LPS.Memory_CD4_T_cells_STAT1                Unpaired only
## LPS.Memory_CD4_T_cells_STAT3              Not significant
## LPS.Memory_CD4_T_cells_S6                 Not significant
## LPS.Memory_CD4_T_cells_MAPKAPK2           Not significant
## LPS.Memory_CD4_T_cells_IkB                Not significant
## LPS.Memory_CD4_T_cells_NFkB               Not significant
## LPS.Memory_CD4_T_cells_ERK                Not significant
## Cocktail.Granulocytes_CREB                Not significant
## Cocktail.Granulocytes_STAT5               Not significant
## Cocktail.Granulocytes_p38                     Paired only
## Cocktail.Granulocytes_STAT1                          Both
## Cocktail.Granulocytes_STAT3               Not significant
## Cocktail.Granulocytes_S6                  Not significant
## Cocktail.Granulocytes_MAPKAPK2            Not significant
## Cocktail.Granulocytes_IkB                 Not significant
## Cocktail.Granulocytes_NFkB                           Both
## Cocktail.Granulocytes_ERK                 Not significant
## Cocktail.CD8_T_cells_CREB                 Not significant
## Cocktail.CD8_T_cells_STAT5                           Both
## Cocktail.CD8_T_cells_p38                  Not significant
## Cocktail.CD8_T_cells_STAT1                Not significant
## Cocktail.CD8_T_cells_STAT3                           Both
## Cocktail.CD8_T_cells_S6                   Not significant
## Cocktail.CD8_T_cells_MAPKAPK2             Not significant
## Cocktail.CD8_T_cells_IkB                  Not significant
## Cocktail.CD8_T_cells_NFkB                 Not significant
## Cocktail.CD8_T_cells_ERK                  Not significant
## Cocktail.CD4_T_cells_CREB                 Not significant
## Cocktail.CD4_T_cells_STAT5                           Both
## Cocktail.CD4_T_cells_p38                  Not significant
## Cocktail.CD4_T_cells_STAT1                           Both
## Cocktail.CD4_T_cells_STAT3                Not significant
## Cocktail.CD4_T_cells_S6                   Not significant
## Cocktail.CD4_T_cells_MAPKAPK2             Not significant
## Cocktail.CD4_T_cells_IkB                  Not significant
## Cocktail.CD4_T_cells_NFkB                 Not significant
## Cocktail.CD4_T_cells_ERK                  Not significant
## Cocktail.Naive_CD4_T_cells_CREB           Not significant
## Cocktail.Naive_CD4_T_cells_STAT5                     Both
## Cocktail.Naive_CD4_T_cells_p38            Not significant
## Cocktail.Naive_CD4_T_cells_STAT1                     Both
## Cocktail.Naive_CD4_T_cells_STAT3          Not significant
## Cocktail.Naive_CD4_T_cells_S6             Not significant
## Cocktail.Naive_CD4_T_cells_MAPKAPK2       Not significant
## Cocktail.Naive_CD4_T_cells_IkB            Not significant
## Cocktail.Naive_CD4_T_cells_NFkB           Not significant
## Cocktail.Naive_CD4_T_cells_ERK            Not significant
## Cocktail.Naive_CD8_T_cells_CREB           Not significant
## Cocktail.Naive_CD8_T_cells_STAT5                     Both
## Cocktail.Naive_CD8_T_cells_p38            Not significant
## Cocktail.Naive_CD8_T_cells_STAT1                     Both
## Cocktail.Naive_CD8_T_cells_STAT3          Not significant
## Cocktail.Naive_CD8_T_cells_S6             Not significant
## Cocktail.Naive_CD8_T_cells_MAPKAPK2       Not significant
## Cocktail.Naive_CD8_T_cells_IkB            Not significant
## Cocktail.Naive_CD8_T_cells_NFkB           Not significant
## Cocktail.Naive_CD8_T_cells_ERK            Not significant
## Cocktail.Memory_CD8_T_cells_CREB                     Both
## Cocktail.Memory_CD8_T_cells_STAT5         Not significant
## Cocktail.Memory_CD8_T_cells_p38           Not significant
## Cocktail.Memory_CD8_T_cells_STAT1         Not significant
## Cocktail.Memory_CD8_T_cells_STAT3                    Both
## Cocktail.Memory_CD8_T_cells_S6                       Both
## Cocktail.Memory_CD8_T_cells_MAPKAPK2      Not significant
## Cocktail.Memory_CD8_T_cells_IkB           Not significant
## Cocktail.Memory_CD8_T_cells_NFkB          Not significant
## Cocktail.Memory_CD8_T_cells_ERK           Not significant
## Cocktail.B_cells_CREB                     Not significant
## Cocktail.B_cells_STAT5                    Not significant
## Cocktail.B_cells_p38                      Not significant
## Cocktail.B_cells_STAT1                               Both
## Cocktail.B_cells_STAT3                    Not significant
## Cocktail.B_cells_S6                       Not significant
## Cocktail.B_cells_MAPKAPK2                 Not significant
## Cocktail.B_cells_IkB                      Not significant
## Cocktail.B_cells_NFkB                     Not significant
## Cocktail.B_cells_ERK                      Not significant
## Cocktail.Classical_monocytes_CREB         Not significant
## Cocktail.Classical_monocytes_STAT5        Not significant
## Cocktail.Classical_monocytes_p38          Not significant
## Cocktail.Classical_monocytes_STAT1                   Both
## Cocktail.Classical_monocytes_STAT3                   Both
## Cocktail.Classical_monocytes_S6           Not significant
## Cocktail.Classical_monocytes_MAPKAPK2     Not significant
## Cocktail.Classical_monocytes_IkB          Not significant
## Cocktail.Classical_monocytes_NFkB         Not significant
## Cocktail.Classical_monocytes_ERK          Not significant
## Cocktail.Nonclassical_monocytes_CREB                 Both
## Cocktail.Nonclassical_monocytes_STAT5     Not significant
## Cocktail.Nonclassical_monocytes_p38       Not significant
## Cocktail.Nonclassical_monocytes_STAT1         Paired only
## Cocktail.Nonclassical_monocytes_STAT3     Not significant
## Cocktail.Nonclassical_monocytes_S6                   Both
## Cocktail.Nonclassical_monocytes_MAPKAPK2  Not significant
## Cocktail.Nonclassical_monocytes_IkB       Not significant
## Cocktail.Nonclassical_monocytes_NFkB      Not significant
## Cocktail.Nonclassical_monocytes_ERK       Not significant
## Cocktail.cDCs_CREB                        Not significant
## Cocktail.cDCs_STAT5                       Not significant
## Cocktail.cDCs_p38                         Not significant
## Cocktail.cDCs_STAT1                                  Both
## Cocktail.cDCs_STAT3                                  Both
## Cocktail.cDCs_S6                          Not significant
## Cocktail.cDCs_MAPKAPK2                    Not significant
## Cocktail.cDCs_IkB                         Not significant
## Cocktail.cDCs_NFkB                        Not significant
## Cocktail.cDCs_ERK                         Not significant
## Cocktail.pDCs_CREB                        Not significant
## Cocktail.pDCs_STAT5                                  Both
## Cocktail.pDCs_p38                         Not significant
## Cocktail.pDCs_STAT1                                  Both
## Cocktail.pDCs_STAT3                                  Both
## Cocktail.pDCs_S6                          Not significant
## Cocktail.pDCs_MAPKAPK2                    Not significant
## Cocktail.pDCs_IkB                         Not significant
## Cocktail.pDCs_NFkB                        Not significant
## Cocktail.pDCs_ERK                                    Both
## Cocktail.Th1_T_cells_CREB                 Not significant
## Cocktail.Th1_T_cells_STAT5                Not significant
## Cocktail.Th1_T_cells_p38                  Not significant
## Cocktail.Th1_T_cells_STAT1                Not significant
## Cocktail.Th1_T_cells_STAT3                Not significant
## Cocktail.Th1_T_cells_S6                   Not significant
## Cocktail.Th1_T_cells_MAPKAPK2             Not significant
## Cocktail.Th1_T_cells_IkB                  Not significant
## Cocktail.Th1_T_cells_NFkB                 Not significant
## Cocktail.Th1_T_cells_ERK                             Both
## Cocktail.Intermediate_monocytes_CREB                 Both
## Cocktail.Intermediate_monocytes_STAT5     Not significant
## Cocktail.Intermediate_monocytes_p38       Not significant
## Cocktail.Intermediate_monocytes_STAT1                Both
## Cocktail.Intermediate_monocytes_STAT3                Both
## Cocktail.Intermediate_monocytes_S6                   Both
## Cocktail.Intermediate_monocytes_MAPKAPK2             Both
## Cocktail.Intermediate_monocytes_IkB       Not significant
## Cocktail.Intermediate_monocytes_NFkB      Not significant
## Cocktail.Intermediate_monocytes_ERK       Not significant
## Cocktail.MDSCs_CREB                       Not significant
## Cocktail.MDSCs_STAT5                      Not significant
## Cocktail.MDSCs_p38                        Not significant
## Cocktail.MDSCs_STAT1                                 Both
## Cocktail.MDSCs_STAT3                                 Both
## Cocktail.MDSCs_S6                         Not significant
## Cocktail.MDSCs_MAPKAPK2                   Not significant
## Cocktail.MDSCs_IkB                        Not significant
## Cocktail.MDSCs_NFkB                       Not significant
## Cocktail.MDSCs_ERK                        Not significant
## Cocktail.Tregs_CREB                       Not significant
## Cocktail.Tregs_STAT5                      Not significant
## Cocktail.Tregs_p38                        Not significant
## Cocktail.Tregs_STAT1                                 Both
## Cocktail.Tregs_STAT3                      Not significant
## Cocktail.Tregs_S6                         Not significant
## Cocktail.Tregs_MAPKAPK2                   Not significant
## Cocktail.Tregs_IkB                        Not significant
## Cocktail.Tregs_NFkB                       Not significant
## Cocktail.Tregs_ERK                        Not significant
## Cocktail.CD56lo_NK_cells_CREB                        Both
## Cocktail.CD56lo_NK_cells_STAT5            Not significant
## Cocktail.CD56lo_NK_cells_p38              Not significant
## Cocktail.CD56lo_NK_cells_STAT1                       Both
## Cocktail.CD56lo_NK_cells_STAT3                       Both
## Cocktail.CD56lo_NK_cells_S6                   Paired only
## Cocktail.CD56lo_NK_cells_MAPKAPK2         Not significant
## Cocktail.CD56lo_NK_cells_IkB              Not significant
## Cocktail.CD56lo_NK_cells_NFkB             Not significant
## Cocktail.CD56lo_NK_cells_ERK                  Paired only
## Cocktail.CD56hi_NK_cells_CREB             Not significant
## Cocktail.CD56hi_NK_cells_STAT5            Not significant
## Cocktail.CD56hi_NK_cells_p38              Not significant
## Cocktail.CD56hi_NK_cells_STAT1                       Both
## Cocktail.CD56hi_NK_cells_STAT3            Not significant
## Cocktail.CD56hi_NK_cells_S6               Not significant
## Cocktail.CD56hi_NK_cells_MAPKAPK2                    Both
## Cocktail.CD56hi_NK_cells_IkB              Not significant
## Cocktail.CD56hi_NK_cells_NFkB             Not significant
## Cocktail.CD56hi_NK_cells_ERK              Not significant
## Cocktail.gd_T_cells_CREB                    Unpaired only
## Cocktail.gd_T_cells_STAT5                            Both
## Cocktail.gd_T_cells_p38                   Not significant
## Cocktail.gd_T_cells_STAT1                            Both
## Cocktail.gd_T_cells_STAT3                     Paired only
## Cocktail.gd_T_cells_S6                    Not significant
## Cocktail.gd_T_cells_MAPKAPK2              Not significant
## Cocktail.gd_T_cells_IkB                   Not significant
## Cocktail.gd_T_cells_NFkB                  Not significant
## Cocktail.gd_T_cells_ERK                   Not significant
## Cocktail.Memory_CD4_T_cells_CREB          Not significant
## Cocktail.Memory_CD4_T_cells_STAT5                    Both
## Cocktail.Memory_CD4_T_cells_p38           Not significant
## Cocktail.Memory_CD4_T_cells_STAT1                    Both
## Cocktail.Memory_CD4_T_cells_STAT3         Not significant
## Cocktail.Memory_CD4_T_cells_S6            Not significant
## Cocktail.Memory_CD4_T_cells_MAPKAPK2      Not significant
## Cocktail.Memory_CD4_T_cells_IkB           Not significant
## Cocktail.Memory_CD4_T_cells_NFkB          Not significant
## Cocktail.Memory_CD4_T_cells_ERK           Not significant
##                                                                          Features
## LPS.Granulocytes_CREB                                       LPS.Granulocytes_CREB
## LPS.Granulocytes_STAT5                                     LPS.Granulocytes_STAT5
## LPS.Granulocytes_p38                                         LPS.Granulocytes_p38
## LPS.Granulocytes_STAT1                                     LPS.Granulocytes_STAT1
## LPS.Granulocytes_STAT3                                     LPS.Granulocytes_STAT3
## LPS.Granulocytes_S6                                           LPS.Granulocytes_S6
## LPS.Granulocytes_MAPKAPK2                               LPS.Granulocytes_MAPKAPK2
## LPS.Granulocytes_IkB                                         LPS.Granulocytes_IkB
## LPS.Granulocytes_NFkB                                       LPS.Granulocytes_NFkB
## LPS.Granulocytes_ERK                                         LPS.Granulocytes_ERK
## LPS.CD8_T_cells_CREB                                         LPS.CD8_T_cells_CREB
## LPS.CD8_T_cells_STAT5                                       LPS.CD8_T_cells_STAT5
## LPS.CD8_T_cells_p38                                           LPS.CD8_T_cells_p38
## LPS.CD8_T_cells_STAT1                                       LPS.CD8_T_cells_STAT1
## LPS.CD8_T_cells_STAT3                                       LPS.CD8_T_cells_STAT3
## LPS.CD8_T_cells_S6                                             LPS.CD8_T_cells_S6
## LPS.CD8_T_cells_MAPKAPK2                                 LPS.CD8_T_cells_MAPKAPK2
## LPS.CD8_T_cells_IkB                                           LPS.CD8_T_cells_IkB
## LPS.CD8_T_cells_NFkB                                         LPS.CD8_T_cells_NFkB
## LPS.CD8_T_cells_ERK                                           LPS.CD8_T_cells_ERK
## LPS.CD4_T_cells_CREB                                         LPS.CD4_T_cells_CREB
## LPS.CD4_T_cells_STAT5                                       LPS.CD4_T_cells_STAT5
## LPS.CD4_T_cells_p38                                           LPS.CD4_T_cells_p38
## LPS.CD4_T_cells_STAT1                                       LPS.CD4_T_cells_STAT1
## LPS.CD4_T_cells_STAT3                                       LPS.CD4_T_cells_STAT3
## LPS.CD4_T_cells_S6                                             LPS.CD4_T_cells_S6
## LPS.CD4_T_cells_MAPKAPK2                                 LPS.CD4_T_cells_MAPKAPK2
## LPS.CD4_T_cells_IkB                                           LPS.CD4_T_cells_IkB
## LPS.CD4_T_cells_NFkB                                         LPS.CD4_T_cells_NFkB
## LPS.CD4_T_cells_ERK                                           LPS.CD4_T_cells_ERK
## LPS.Naive_CD4_T_cells_CREB                             LPS.Naive_CD4_T_cells_CREB
## LPS.Naive_CD4_T_cells_STAT5                           LPS.Naive_CD4_T_cells_STAT5
## LPS.Naive_CD4_T_cells_p38                               LPS.Naive_CD4_T_cells_p38
## LPS.Naive_CD4_T_cells_STAT1                           LPS.Naive_CD4_T_cells_STAT1
## LPS.Naive_CD4_T_cells_STAT3                           LPS.Naive_CD4_T_cells_STAT3
## LPS.Naive_CD4_T_cells_S6                                 LPS.Naive_CD4_T_cells_S6
## LPS.Naive_CD4_T_cells_MAPKAPK2                     LPS.Naive_CD4_T_cells_MAPKAPK2
## LPS.Naive_CD4_T_cells_IkB                               LPS.Naive_CD4_T_cells_IkB
## LPS.Naive_CD4_T_cells_NFkB                             LPS.Naive_CD4_T_cells_NFkB
## LPS.Naive_CD4_T_cells_ERK                               LPS.Naive_CD4_T_cells_ERK
## LPS.Naive_CD8_T_cells_CREB                             LPS.Naive_CD8_T_cells_CREB
## LPS.Naive_CD8_T_cells_STAT5                           LPS.Naive_CD8_T_cells_STAT5
## LPS.Naive_CD8_T_cells_p38                               LPS.Naive_CD8_T_cells_p38
## LPS.Naive_CD8_T_cells_STAT1                           LPS.Naive_CD8_T_cells_STAT1
## LPS.Naive_CD8_T_cells_STAT3                           LPS.Naive_CD8_T_cells_STAT3
## LPS.Naive_CD8_T_cells_S6                                 LPS.Naive_CD8_T_cells_S6
## LPS.Naive_CD8_T_cells_MAPKAPK2                     LPS.Naive_CD8_T_cells_MAPKAPK2
## LPS.Naive_CD8_T_cells_IkB                               LPS.Naive_CD8_T_cells_IkB
## LPS.Naive_CD8_T_cells_NFkB                             LPS.Naive_CD8_T_cells_NFkB
## LPS.Naive_CD8_T_cells_ERK                               LPS.Naive_CD8_T_cells_ERK
## LPS.Memory_CD8_T_cells_CREB                           LPS.Memory_CD8_T_cells_CREB
## LPS.Memory_CD8_T_cells_STAT5                         LPS.Memory_CD8_T_cells_STAT5
## LPS.Memory_CD8_T_cells_p38                             LPS.Memory_CD8_T_cells_p38
## LPS.Memory_CD8_T_cells_STAT1                         LPS.Memory_CD8_T_cells_STAT1
## LPS.Memory_CD8_T_cells_STAT3                         LPS.Memory_CD8_T_cells_STAT3
## LPS.Memory_CD8_T_cells_S6                               LPS.Memory_CD8_T_cells_S6
## LPS.Memory_CD8_T_cells_MAPKAPK2                   LPS.Memory_CD8_T_cells_MAPKAPK2
## LPS.Memory_CD8_T_cells_IkB                             LPS.Memory_CD8_T_cells_IkB
## LPS.Memory_CD8_T_cells_NFkB                           LPS.Memory_CD8_T_cells_NFkB
## LPS.Memory_CD8_T_cells_ERK                             LPS.Memory_CD8_T_cells_ERK
## LPS.B_cells_CREB                                                 LPS.B_cells_CREB
## LPS.B_cells_STAT5                                               LPS.B_cells_STAT5
## LPS.B_cells_p38                                                   LPS.B_cells_p38
## LPS.B_cells_STAT1                                               LPS.B_cells_STAT1
## LPS.B_cells_STAT3                                               LPS.B_cells_STAT3
## LPS.B_cells_S6                                                     LPS.B_cells_S6
## LPS.B_cells_MAPKAPK2                                         LPS.B_cells_MAPKAPK2
## LPS.B_cells_IkB                                                   LPS.B_cells_IkB
## LPS.B_cells_NFkB                                                 LPS.B_cells_NFkB
## LPS.B_cells_ERK                                                   LPS.B_cells_ERK
## LPS.Classical_monocytes_CREB                         LPS.Classical_monocytes_CREB
## LPS.Classical_monocytes_STAT5                       LPS.Classical_monocytes_STAT5
## LPS.Classical_monocytes_p38                           LPS.Classical_monocytes_p38
## LPS.Classical_monocytes_STAT1                       LPS.Classical_monocytes_STAT1
## LPS.Classical_monocytes_STAT3                       LPS.Classical_monocytes_STAT3
## LPS.Classical_monocytes_S6                             LPS.Classical_monocytes_S6
## LPS.Classical_monocytes_MAPKAPK2                 LPS.Classical_monocytes_MAPKAPK2
## LPS.Classical_monocytes_IkB                           LPS.Classical_monocytes_IkB
## LPS.Classical_monocytes_NFkB                         LPS.Classical_monocytes_NFkB
## LPS.Classical_monocytes_ERK                           LPS.Classical_monocytes_ERK
## LPS.Nonclassical_monocytes_CREB                   LPS.Nonclassical_monocytes_CREB
## LPS.Nonclassical_monocytes_STAT5                 LPS.Nonclassical_monocytes_STAT5
## LPS.Nonclassical_monocytes_p38                     LPS.Nonclassical_monocytes_p38
## LPS.Nonclassical_monocytes_STAT1                 LPS.Nonclassical_monocytes_STAT1
## LPS.Nonclassical_monocytes_STAT3                 LPS.Nonclassical_monocytes_STAT3
## LPS.Nonclassical_monocytes_S6                       LPS.Nonclassical_monocytes_S6
## LPS.Nonclassical_monocytes_MAPKAPK2           LPS.Nonclassical_monocytes_MAPKAPK2
## LPS.Nonclassical_monocytes_IkB                     LPS.Nonclassical_monocytes_IkB
## LPS.Nonclassical_monocytes_NFkB                   LPS.Nonclassical_monocytes_NFkB
## LPS.Nonclassical_monocytes_ERK                     LPS.Nonclassical_monocytes_ERK
## LPS.cDCs_CREB                                                       LPS.cDCs_CREB
## LPS.cDCs_STAT5                                                     LPS.cDCs_STAT5
## LPS.cDCs_p38                                                         LPS.cDCs_p38
## LPS.cDCs_STAT1                                                     LPS.cDCs_STAT1
## LPS.cDCs_STAT3                                                     LPS.cDCs_STAT3
## LPS.cDCs_S6                                                           LPS.cDCs_S6
## LPS.cDCs_MAPKAPK2                                               LPS.cDCs_MAPKAPK2
## LPS.cDCs_IkB                                                         LPS.cDCs_IkB
## LPS.cDCs_NFkB                                                       LPS.cDCs_NFkB
## LPS.cDCs_ERK                                                         LPS.cDCs_ERK
## LPS.pDCs_CREB                                                       LPS.pDCs_CREB
## LPS.pDCs_STAT5                                                     LPS.pDCs_STAT5
## LPS.pDCs_p38                                                         LPS.pDCs_p38
## LPS.pDCs_STAT1                                                     LPS.pDCs_STAT1
## LPS.pDCs_STAT3                                                     LPS.pDCs_STAT3
## LPS.pDCs_S6                                                           LPS.pDCs_S6
## LPS.pDCs_MAPKAPK2                                               LPS.pDCs_MAPKAPK2
## LPS.pDCs_IkB                                                         LPS.pDCs_IkB
## LPS.pDCs_NFkB                                                       LPS.pDCs_NFkB
## LPS.pDCs_ERK                                                         LPS.pDCs_ERK
## LPS.Th1_T_cells_CREB                                         LPS.Th1_T_cells_CREB
## LPS.Th1_T_cells_STAT5                                       LPS.Th1_T_cells_STAT5
## LPS.Th1_T_cells_p38                                           LPS.Th1_T_cells_p38
## LPS.Th1_T_cells_STAT1                                       LPS.Th1_T_cells_STAT1
## LPS.Th1_T_cells_STAT3                                       LPS.Th1_T_cells_STAT3
## LPS.Th1_T_cells_S6                                             LPS.Th1_T_cells_S6
## LPS.Th1_T_cells_MAPKAPK2                                 LPS.Th1_T_cells_MAPKAPK2
## LPS.Th1_T_cells_IkB                                           LPS.Th1_T_cells_IkB
## LPS.Th1_T_cells_NFkB                                         LPS.Th1_T_cells_NFkB
## LPS.Th1_T_cells_ERK                                           LPS.Th1_T_cells_ERK
## LPS.Intermediate_monocytes_CREB                   LPS.Intermediate_monocytes_CREB
## LPS.Intermediate_monocytes_STAT5                 LPS.Intermediate_monocytes_STAT5
## LPS.Intermediate_monocytes_p38                     LPS.Intermediate_monocytes_p38
## LPS.Intermediate_monocytes_STAT1                 LPS.Intermediate_monocytes_STAT1
## LPS.Intermediate_monocytes_STAT3                 LPS.Intermediate_monocytes_STAT3
## LPS.Intermediate_monocytes_S6                       LPS.Intermediate_monocytes_S6
## LPS.Intermediate_monocytes_MAPKAPK2           LPS.Intermediate_monocytes_MAPKAPK2
## LPS.Intermediate_monocytes_IkB                     LPS.Intermediate_monocytes_IkB
## LPS.Intermediate_monocytes_NFkB                   LPS.Intermediate_monocytes_NFkB
## LPS.Intermediate_monocytes_ERK                     LPS.Intermediate_monocytes_ERK
## LPS.MDSCs_CREB                                                     LPS.MDSCs_CREB
## LPS.MDSCs_STAT5                                                   LPS.MDSCs_STAT5
## LPS.MDSCs_p38                                                       LPS.MDSCs_p38
## LPS.MDSCs_STAT1                                                   LPS.MDSCs_STAT1
## LPS.MDSCs_STAT3                                                   LPS.MDSCs_STAT3
## LPS.MDSCs_S6                                                         LPS.MDSCs_S6
## LPS.MDSCs_MAPKAPK2                                             LPS.MDSCs_MAPKAPK2
## LPS.MDSCs_IkB                                                       LPS.MDSCs_IkB
## LPS.MDSCs_NFkB                                                     LPS.MDSCs_NFkB
## LPS.MDSCs_ERK                                                       LPS.MDSCs_ERK
## LPS.Tregs_CREB                                                     LPS.Tregs_CREB
## LPS.Tregs_STAT5                                                   LPS.Tregs_STAT5
## LPS.Tregs_p38                                                       LPS.Tregs_p38
## LPS.Tregs_STAT1                                                   LPS.Tregs_STAT1
## LPS.Tregs_STAT3                                                   LPS.Tregs_STAT3
## LPS.Tregs_S6                                                         LPS.Tregs_S6
## LPS.Tregs_MAPKAPK2                                             LPS.Tregs_MAPKAPK2
## LPS.Tregs_IkB                                                       LPS.Tregs_IkB
## LPS.Tregs_NFkB                                                     LPS.Tregs_NFkB
## LPS.Tregs_ERK                                                       LPS.Tregs_ERK
## LPS.CD56lo_NK_cells_CREB                                 LPS.CD56lo_NK_cells_CREB
## LPS.CD56lo_NK_cells_STAT5                               LPS.CD56lo_NK_cells_STAT5
## LPS.CD56lo_NK_cells_p38                                   LPS.CD56lo_NK_cells_p38
## LPS.CD56lo_NK_cells_STAT1                               LPS.CD56lo_NK_cells_STAT1
## LPS.CD56lo_NK_cells_STAT3                               LPS.CD56lo_NK_cells_STAT3
## LPS.CD56lo_NK_cells_S6                                     LPS.CD56lo_NK_cells_S6
## LPS.CD56lo_NK_cells_MAPKAPK2                         LPS.CD56lo_NK_cells_MAPKAPK2
## LPS.CD56lo_NK_cells_IkB                                   LPS.CD56lo_NK_cells_IkB
## LPS.CD56lo_NK_cells_NFkB                                 LPS.CD56lo_NK_cells_NFkB
## LPS.CD56lo_NK_cells_ERK                                   LPS.CD56lo_NK_cells_ERK
## LPS.CD56hi_NK_cells_CREB                                 LPS.CD56hi_NK_cells_CREB
## LPS.CD56hi_NK_cells_STAT5                               LPS.CD56hi_NK_cells_STAT5
## LPS.CD56hi_NK_cells_p38                                   LPS.CD56hi_NK_cells_p38
## LPS.CD56hi_NK_cells_STAT1                               LPS.CD56hi_NK_cells_STAT1
## LPS.CD56hi_NK_cells_STAT3                               LPS.CD56hi_NK_cells_STAT3
## LPS.CD56hi_NK_cells_S6                                     LPS.CD56hi_NK_cells_S6
## LPS.CD56hi_NK_cells_MAPKAPK2                         LPS.CD56hi_NK_cells_MAPKAPK2
## LPS.CD56hi_NK_cells_IkB                                   LPS.CD56hi_NK_cells_IkB
## LPS.CD56hi_NK_cells_NFkB                                 LPS.CD56hi_NK_cells_NFkB
## LPS.CD56hi_NK_cells_ERK                                   LPS.CD56hi_NK_cells_ERK
## LPS.gd_T_cells_CREB                                           LPS.gd_T_cells_CREB
## LPS.gd_T_cells_STAT5                                         LPS.gd_T_cells_STAT5
## LPS.gd_T_cells_p38                                             LPS.gd_T_cells_p38
## LPS.gd_T_cells_STAT1                                         LPS.gd_T_cells_STAT1
## LPS.gd_T_cells_STAT3                                         LPS.gd_T_cells_STAT3
## LPS.gd_T_cells_S6                                               LPS.gd_T_cells_S6
## LPS.gd_T_cells_MAPKAPK2                                   LPS.gd_T_cells_MAPKAPK2
## LPS.gd_T_cells_IkB                                             LPS.gd_T_cells_IkB
## LPS.gd_T_cells_NFkB                                           LPS.gd_T_cells_NFkB
## LPS.gd_T_cells_ERK                                             LPS.gd_T_cells_ERK
## LPS.Memory_CD4_T_cells_CREB                           LPS.Memory_CD4_T_cells_CREB
## LPS.Memory_CD4_T_cells_STAT5                         LPS.Memory_CD4_T_cells_STAT5
## LPS.Memory_CD4_T_cells_p38                             LPS.Memory_CD4_T_cells_p38
## LPS.Memory_CD4_T_cells_STAT1                         LPS.Memory_CD4_T_cells_STAT1
## LPS.Memory_CD4_T_cells_STAT3                         LPS.Memory_CD4_T_cells_STAT3
## LPS.Memory_CD4_T_cells_S6                               LPS.Memory_CD4_T_cells_S6
## LPS.Memory_CD4_T_cells_MAPKAPK2                   LPS.Memory_CD4_T_cells_MAPKAPK2
## LPS.Memory_CD4_T_cells_IkB                             LPS.Memory_CD4_T_cells_IkB
## LPS.Memory_CD4_T_cells_NFkB                           LPS.Memory_CD4_T_cells_NFkB
## LPS.Memory_CD4_T_cells_ERK                             LPS.Memory_CD4_T_cells_ERK
## Cocktail.Granulocytes_CREB                             Cocktail.Granulocytes_CREB
## Cocktail.Granulocytes_STAT5                           Cocktail.Granulocytes_STAT5
## Cocktail.Granulocytes_p38                               Cocktail.Granulocytes_p38
## Cocktail.Granulocytes_STAT1                           Cocktail.Granulocytes_STAT1
## Cocktail.Granulocytes_STAT3                           Cocktail.Granulocytes_STAT3
## Cocktail.Granulocytes_S6                                 Cocktail.Granulocytes_S6
## Cocktail.Granulocytes_MAPKAPK2                     Cocktail.Granulocytes_MAPKAPK2
## Cocktail.Granulocytes_IkB                               Cocktail.Granulocytes_IkB
## Cocktail.Granulocytes_NFkB                             Cocktail.Granulocytes_NFkB
## Cocktail.Granulocytes_ERK                               Cocktail.Granulocytes_ERK
## Cocktail.CD8_T_cells_CREB                               Cocktail.CD8_T_cells_CREB
## Cocktail.CD8_T_cells_STAT5                             Cocktail.CD8_T_cells_STAT5
## Cocktail.CD8_T_cells_p38                                 Cocktail.CD8_T_cells_p38
## Cocktail.CD8_T_cells_STAT1                             Cocktail.CD8_T_cells_STAT1
## Cocktail.CD8_T_cells_STAT3                             Cocktail.CD8_T_cells_STAT3
## Cocktail.CD8_T_cells_S6                                   Cocktail.CD8_T_cells_S6
## Cocktail.CD8_T_cells_MAPKAPK2                       Cocktail.CD8_T_cells_MAPKAPK2
## Cocktail.CD8_T_cells_IkB                                 Cocktail.CD8_T_cells_IkB
## Cocktail.CD8_T_cells_NFkB                               Cocktail.CD8_T_cells_NFkB
## Cocktail.CD8_T_cells_ERK                                 Cocktail.CD8_T_cells_ERK
## Cocktail.CD4_T_cells_CREB                               Cocktail.CD4_T_cells_CREB
## Cocktail.CD4_T_cells_STAT5                             Cocktail.CD4_T_cells_STAT5
## Cocktail.CD4_T_cells_p38                                 Cocktail.CD4_T_cells_p38
## Cocktail.CD4_T_cells_STAT1                             Cocktail.CD4_T_cells_STAT1
## Cocktail.CD4_T_cells_STAT3                             Cocktail.CD4_T_cells_STAT3
## Cocktail.CD4_T_cells_S6                                   Cocktail.CD4_T_cells_S6
## Cocktail.CD4_T_cells_MAPKAPK2                       Cocktail.CD4_T_cells_MAPKAPK2
## Cocktail.CD4_T_cells_IkB                                 Cocktail.CD4_T_cells_IkB
## Cocktail.CD4_T_cells_NFkB                               Cocktail.CD4_T_cells_NFkB
## Cocktail.CD4_T_cells_ERK                                 Cocktail.CD4_T_cells_ERK
## Cocktail.Naive_CD4_T_cells_CREB                   Cocktail.Naive_CD4_T_cells_CREB
## Cocktail.Naive_CD4_T_cells_STAT5                 Cocktail.Naive_CD4_T_cells_STAT5
## Cocktail.Naive_CD4_T_cells_p38                     Cocktail.Naive_CD4_T_cells_p38
## Cocktail.Naive_CD4_T_cells_STAT1                 Cocktail.Naive_CD4_T_cells_STAT1
## Cocktail.Naive_CD4_T_cells_STAT3                 Cocktail.Naive_CD4_T_cells_STAT3
## Cocktail.Naive_CD4_T_cells_S6                       Cocktail.Naive_CD4_T_cells_S6
## Cocktail.Naive_CD4_T_cells_MAPKAPK2           Cocktail.Naive_CD4_T_cells_MAPKAPK2
## Cocktail.Naive_CD4_T_cells_IkB                     Cocktail.Naive_CD4_T_cells_IkB
## Cocktail.Naive_CD4_T_cells_NFkB                   Cocktail.Naive_CD4_T_cells_NFkB
## Cocktail.Naive_CD4_T_cells_ERK                     Cocktail.Naive_CD4_T_cells_ERK
## Cocktail.Naive_CD8_T_cells_CREB                   Cocktail.Naive_CD8_T_cells_CREB
## Cocktail.Naive_CD8_T_cells_STAT5                 Cocktail.Naive_CD8_T_cells_STAT5
## Cocktail.Naive_CD8_T_cells_p38                     Cocktail.Naive_CD8_T_cells_p38
## Cocktail.Naive_CD8_T_cells_STAT1                 Cocktail.Naive_CD8_T_cells_STAT1
## Cocktail.Naive_CD8_T_cells_STAT3                 Cocktail.Naive_CD8_T_cells_STAT3
## Cocktail.Naive_CD8_T_cells_S6                       Cocktail.Naive_CD8_T_cells_S6
## Cocktail.Naive_CD8_T_cells_MAPKAPK2           Cocktail.Naive_CD8_T_cells_MAPKAPK2
## Cocktail.Naive_CD8_T_cells_IkB                     Cocktail.Naive_CD8_T_cells_IkB
## Cocktail.Naive_CD8_T_cells_NFkB                   Cocktail.Naive_CD8_T_cells_NFkB
## Cocktail.Naive_CD8_T_cells_ERK                     Cocktail.Naive_CD8_T_cells_ERK
## Cocktail.Memory_CD8_T_cells_CREB                 Cocktail.Memory_CD8_T_cells_CREB
## Cocktail.Memory_CD8_T_cells_STAT5               Cocktail.Memory_CD8_T_cells_STAT5
## Cocktail.Memory_CD8_T_cells_p38                   Cocktail.Memory_CD8_T_cells_p38
## Cocktail.Memory_CD8_T_cells_STAT1               Cocktail.Memory_CD8_T_cells_STAT1
## Cocktail.Memory_CD8_T_cells_STAT3               Cocktail.Memory_CD8_T_cells_STAT3
## Cocktail.Memory_CD8_T_cells_S6                     Cocktail.Memory_CD8_T_cells_S6
## Cocktail.Memory_CD8_T_cells_MAPKAPK2         Cocktail.Memory_CD8_T_cells_MAPKAPK2
## Cocktail.Memory_CD8_T_cells_IkB                   Cocktail.Memory_CD8_T_cells_IkB
## Cocktail.Memory_CD8_T_cells_NFkB                 Cocktail.Memory_CD8_T_cells_NFkB
## Cocktail.Memory_CD8_T_cells_ERK                   Cocktail.Memory_CD8_T_cells_ERK
## Cocktail.B_cells_CREB                                       Cocktail.B_cells_CREB
## Cocktail.B_cells_STAT5                                     Cocktail.B_cells_STAT5
## Cocktail.B_cells_p38                                         Cocktail.B_cells_p38
## Cocktail.B_cells_STAT1                                     Cocktail.B_cells_STAT1
## Cocktail.B_cells_STAT3                                     Cocktail.B_cells_STAT3
## Cocktail.B_cells_S6                                           Cocktail.B_cells_S6
## Cocktail.B_cells_MAPKAPK2                               Cocktail.B_cells_MAPKAPK2
## Cocktail.B_cells_IkB                                         Cocktail.B_cells_IkB
## Cocktail.B_cells_NFkB                                       Cocktail.B_cells_NFkB
## Cocktail.B_cells_ERK                                         Cocktail.B_cells_ERK
## Cocktail.Classical_monocytes_CREB               Cocktail.Classical_monocytes_CREB
## Cocktail.Classical_monocytes_STAT5             Cocktail.Classical_monocytes_STAT5
## Cocktail.Classical_monocytes_p38                 Cocktail.Classical_monocytes_p38
## Cocktail.Classical_monocytes_STAT1             Cocktail.Classical_monocytes_STAT1
## Cocktail.Classical_monocytes_STAT3             Cocktail.Classical_monocytes_STAT3
## Cocktail.Classical_monocytes_S6                   Cocktail.Classical_monocytes_S6
## Cocktail.Classical_monocytes_MAPKAPK2       Cocktail.Classical_monocytes_MAPKAPK2
## Cocktail.Classical_monocytes_IkB                 Cocktail.Classical_monocytes_IkB
## Cocktail.Classical_monocytes_NFkB               Cocktail.Classical_monocytes_NFkB
## Cocktail.Classical_monocytes_ERK                 Cocktail.Classical_monocytes_ERK
## Cocktail.Nonclassical_monocytes_CREB         Cocktail.Nonclassical_monocytes_CREB
## Cocktail.Nonclassical_monocytes_STAT5       Cocktail.Nonclassical_monocytes_STAT5
## Cocktail.Nonclassical_monocytes_p38           Cocktail.Nonclassical_monocytes_p38
## Cocktail.Nonclassical_monocytes_STAT1       Cocktail.Nonclassical_monocytes_STAT1
## Cocktail.Nonclassical_monocytes_STAT3       Cocktail.Nonclassical_monocytes_STAT3
## Cocktail.Nonclassical_monocytes_S6             Cocktail.Nonclassical_monocytes_S6
## Cocktail.Nonclassical_monocytes_MAPKAPK2 Cocktail.Nonclassical_monocytes_MAPKAPK2
## Cocktail.Nonclassical_monocytes_IkB           Cocktail.Nonclassical_monocytes_IkB
## Cocktail.Nonclassical_monocytes_NFkB         Cocktail.Nonclassical_monocytes_NFkB
## Cocktail.Nonclassical_monocytes_ERK           Cocktail.Nonclassical_monocytes_ERK
## Cocktail.cDCs_CREB                                             Cocktail.cDCs_CREB
## Cocktail.cDCs_STAT5                                           Cocktail.cDCs_STAT5
## Cocktail.cDCs_p38                                               Cocktail.cDCs_p38
## Cocktail.cDCs_STAT1                                           Cocktail.cDCs_STAT1
## Cocktail.cDCs_STAT3                                           Cocktail.cDCs_STAT3
## Cocktail.cDCs_S6                                                 Cocktail.cDCs_S6
## Cocktail.cDCs_MAPKAPK2                                     Cocktail.cDCs_MAPKAPK2
## Cocktail.cDCs_IkB                                               Cocktail.cDCs_IkB
## Cocktail.cDCs_NFkB                                             Cocktail.cDCs_NFkB
## Cocktail.cDCs_ERK                                               Cocktail.cDCs_ERK
## Cocktail.pDCs_CREB                                             Cocktail.pDCs_CREB
## Cocktail.pDCs_STAT5                                           Cocktail.pDCs_STAT5
## Cocktail.pDCs_p38                                               Cocktail.pDCs_p38
## Cocktail.pDCs_STAT1                                           Cocktail.pDCs_STAT1
## Cocktail.pDCs_STAT3                                           Cocktail.pDCs_STAT3
## Cocktail.pDCs_S6                                                 Cocktail.pDCs_S6
## Cocktail.pDCs_MAPKAPK2                                     Cocktail.pDCs_MAPKAPK2
## Cocktail.pDCs_IkB                                               Cocktail.pDCs_IkB
## Cocktail.pDCs_NFkB                                             Cocktail.pDCs_NFkB
## Cocktail.pDCs_ERK                                               Cocktail.pDCs_ERK
## Cocktail.Th1_T_cells_CREB                               Cocktail.Th1_T_cells_CREB
## Cocktail.Th1_T_cells_STAT5                             Cocktail.Th1_T_cells_STAT5
## Cocktail.Th1_T_cells_p38                                 Cocktail.Th1_T_cells_p38
## Cocktail.Th1_T_cells_STAT1                             Cocktail.Th1_T_cells_STAT1
## Cocktail.Th1_T_cells_STAT3                             Cocktail.Th1_T_cells_STAT3
## Cocktail.Th1_T_cells_S6                                   Cocktail.Th1_T_cells_S6
## Cocktail.Th1_T_cells_MAPKAPK2                       Cocktail.Th1_T_cells_MAPKAPK2
## Cocktail.Th1_T_cells_IkB                                 Cocktail.Th1_T_cells_IkB
## Cocktail.Th1_T_cells_NFkB                               Cocktail.Th1_T_cells_NFkB
## Cocktail.Th1_T_cells_ERK                                 Cocktail.Th1_T_cells_ERK
## Cocktail.Intermediate_monocytes_CREB         Cocktail.Intermediate_monocytes_CREB
## Cocktail.Intermediate_monocytes_STAT5       Cocktail.Intermediate_monocytes_STAT5
## Cocktail.Intermediate_monocytes_p38           Cocktail.Intermediate_monocytes_p38
## Cocktail.Intermediate_monocytes_STAT1       Cocktail.Intermediate_monocytes_STAT1
## Cocktail.Intermediate_monocytes_STAT3       Cocktail.Intermediate_monocytes_STAT3
## Cocktail.Intermediate_monocytes_S6             Cocktail.Intermediate_monocytes_S6
## Cocktail.Intermediate_monocytes_MAPKAPK2 Cocktail.Intermediate_monocytes_MAPKAPK2
## Cocktail.Intermediate_monocytes_IkB           Cocktail.Intermediate_monocytes_IkB
## Cocktail.Intermediate_monocytes_NFkB         Cocktail.Intermediate_monocytes_NFkB
## Cocktail.Intermediate_monocytes_ERK           Cocktail.Intermediate_monocytes_ERK
## Cocktail.MDSCs_CREB                                           Cocktail.MDSCs_CREB
## Cocktail.MDSCs_STAT5                                         Cocktail.MDSCs_STAT5
## Cocktail.MDSCs_p38                                             Cocktail.MDSCs_p38
## Cocktail.MDSCs_STAT1                                         Cocktail.MDSCs_STAT1
## Cocktail.MDSCs_STAT3                                         Cocktail.MDSCs_STAT3
## Cocktail.MDSCs_S6                                               Cocktail.MDSCs_S6
## Cocktail.MDSCs_MAPKAPK2                                   Cocktail.MDSCs_MAPKAPK2
## Cocktail.MDSCs_IkB                                             Cocktail.MDSCs_IkB
## Cocktail.MDSCs_NFkB                                           Cocktail.MDSCs_NFkB
## Cocktail.MDSCs_ERK                                             Cocktail.MDSCs_ERK
## Cocktail.Tregs_CREB                                           Cocktail.Tregs_CREB
## Cocktail.Tregs_STAT5                                         Cocktail.Tregs_STAT5
## Cocktail.Tregs_p38                                             Cocktail.Tregs_p38
## Cocktail.Tregs_STAT1                                         Cocktail.Tregs_STAT1
## Cocktail.Tregs_STAT3                                         Cocktail.Tregs_STAT3
## Cocktail.Tregs_S6                                               Cocktail.Tregs_S6
## Cocktail.Tregs_MAPKAPK2                                   Cocktail.Tregs_MAPKAPK2
## Cocktail.Tregs_IkB                                             Cocktail.Tregs_IkB
## Cocktail.Tregs_NFkB                                           Cocktail.Tregs_NFkB
## Cocktail.Tregs_ERK                                             Cocktail.Tregs_ERK
## Cocktail.CD56lo_NK_cells_CREB                       Cocktail.CD56lo_NK_cells_CREB
## Cocktail.CD56lo_NK_cells_STAT5                     Cocktail.CD56lo_NK_cells_STAT5
## Cocktail.CD56lo_NK_cells_p38                         Cocktail.CD56lo_NK_cells_p38
## Cocktail.CD56lo_NK_cells_STAT1                     Cocktail.CD56lo_NK_cells_STAT1
## Cocktail.CD56lo_NK_cells_STAT3                     Cocktail.CD56lo_NK_cells_STAT3
## Cocktail.CD56lo_NK_cells_S6                           Cocktail.CD56lo_NK_cells_S6
## Cocktail.CD56lo_NK_cells_MAPKAPK2               Cocktail.CD56lo_NK_cells_MAPKAPK2
## Cocktail.CD56lo_NK_cells_IkB                         Cocktail.CD56lo_NK_cells_IkB
## Cocktail.CD56lo_NK_cells_NFkB                       Cocktail.CD56lo_NK_cells_NFkB
## Cocktail.CD56lo_NK_cells_ERK                         Cocktail.CD56lo_NK_cells_ERK
## Cocktail.CD56hi_NK_cells_CREB                       Cocktail.CD56hi_NK_cells_CREB
## Cocktail.CD56hi_NK_cells_STAT5                     Cocktail.CD56hi_NK_cells_STAT5
## Cocktail.CD56hi_NK_cells_p38                         Cocktail.CD56hi_NK_cells_p38
## Cocktail.CD56hi_NK_cells_STAT1                     Cocktail.CD56hi_NK_cells_STAT1
## Cocktail.CD56hi_NK_cells_STAT3                     Cocktail.CD56hi_NK_cells_STAT3
## Cocktail.CD56hi_NK_cells_S6                           Cocktail.CD56hi_NK_cells_S6
## Cocktail.CD56hi_NK_cells_MAPKAPK2               Cocktail.CD56hi_NK_cells_MAPKAPK2
## Cocktail.CD56hi_NK_cells_IkB                         Cocktail.CD56hi_NK_cells_IkB
## Cocktail.CD56hi_NK_cells_NFkB                       Cocktail.CD56hi_NK_cells_NFkB
## Cocktail.CD56hi_NK_cells_ERK                         Cocktail.CD56hi_NK_cells_ERK
## Cocktail.gd_T_cells_CREB                                 Cocktail.gd_T_cells_CREB
## Cocktail.gd_T_cells_STAT5                               Cocktail.gd_T_cells_STAT5
## Cocktail.gd_T_cells_p38                                   Cocktail.gd_T_cells_p38
## Cocktail.gd_T_cells_STAT1                               Cocktail.gd_T_cells_STAT1
## Cocktail.gd_T_cells_STAT3                               Cocktail.gd_T_cells_STAT3
## Cocktail.gd_T_cells_S6                                     Cocktail.gd_T_cells_S6
## Cocktail.gd_T_cells_MAPKAPK2                         Cocktail.gd_T_cells_MAPKAPK2
## Cocktail.gd_T_cells_IkB                                   Cocktail.gd_T_cells_IkB
## Cocktail.gd_T_cells_NFkB                                 Cocktail.gd_T_cells_NFkB
## Cocktail.gd_T_cells_ERK                                   Cocktail.gd_T_cells_ERK
## Cocktail.Memory_CD4_T_cells_CREB                 Cocktail.Memory_CD4_T_cells_CREB
## Cocktail.Memory_CD4_T_cells_STAT5               Cocktail.Memory_CD4_T_cells_STAT5
## Cocktail.Memory_CD4_T_cells_p38                   Cocktail.Memory_CD4_T_cells_p38
## Cocktail.Memory_CD4_T_cells_STAT1               Cocktail.Memory_CD4_T_cells_STAT1
## Cocktail.Memory_CD4_T_cells_STAT3               Cocktail.Memory_CD4_T_cells_STAT3
## Cocktail.Memory_CD4_T_cells_S6                     Cocktail.Memory_CD4_T_cells_S6
## Cocktail.Memory_CD4_T_cells_MAPKAPK2         Cocktail.Memory_CD4_T_cells_MAPKAPK2
## Cocktail.Memory_CD4_T_cells_IkB                   Cocktail.Memory_CD4_T_cells_IkB
## Cocktail.Memory_CD4_T_cells_NFkB                 Cocktail.Memory_CD4_T_cells_NFkB
## Cocktail.Memory_CD4_T_cells_ERK                   Cocktail.Memory_CD4_T_cells_ERK

For abundance:

# for abundance version
mom_df <- percents_df %>% dplyr::filter(SampleType == "M") %>% dplyr::select(-filename, -Pair, -SampleType, -Condition, -Individual)
baby_df <- percents_df %>% dplyr::filter(SampleType == "B") %>% dplyr::select(-filename, -Pair, -SampleType, -Condition, -Individual)
paired_pvals <- mapply(function(x, y) t.test(x,y, paired = TRUE)$p.value, mom_df, baby_df)
unpaired_pvals <- mapply(function(x, y) t.test(x,y, paired = FALSE)$p.value, mom_df, baby_df)

# plot(-log(unpaired_pvals), -log(paired_pvals))

# Number of comparisons: 20 cell types x 10 phosphos x 3 conditions
bonf <- .05/(ncol(mom_df))

significance <- vector(mode = "character", length = length(unpaired_pvals))
significance[(unpaired_pvals < bonf) & (paired_pvals < bonf)] <- "Both"
significance[(unpaired_pvals < bonf) & (paired_pvals > bonf)] <- "Unpaired only"
significance[(unpaired_pvals > bonf) & (paired_pvals < bonf)] <- "Paired only"
significance[(unpaired_pvals > bonf) & (paired_pvals > bonf)] <- "Not significant"

plot_df <- data.frame(unpaired_pvals, paired_pvals, Significance = significance, Features = names(paired_pvals))
p <- ggplot(plot_df, aes(-log(unpaired_pvals), -log(paired_pvals))) + 
  geom_point(size = 1, aes(colour = Significance))  + 
  scale_color_manual(values=c("blue", " dark gray", "red", "orange"))
print(p)

plot_df %>% dplyr::filter(Significance != "Not significant") %>% 
  dplyr::select(-unpaired_pvals) %>%
  dplyr::select(-paired_pvals)

##    Significance                         Features
## 1          Both        CD8_T_cells_Percent_Total
## 2   Paired only Memory_CD8_T_cells_Percent_Total
## 3          Both            B_cells_Percent_Total
## 4 Unpaired only               pDCs_Percent_Total
## 5          Both Memory_CD4_T_cells_Percent_Total
## 6 Unpaired only       Granulocytes_Percent_Total